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Back-end code cleanup, docs, style #91

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Aug 20, 2024
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2 changes: 0 additions & 2 deletions back-end/pyworkflow/pyworkflow/node.py
Original file line number Diff line number Diff line change
Expand Up @@ -48,8 +48,6 @@ def get_execution_options(self, workflow, flow_nodes):
"""
execution_options = dict()

# TODO: Can we iterate through flow_vars instead?
# If none are included, we can just return `self.options`.
for key, option in self.options.items():

if key in flow_nodes:
Expand Down
3 changes: 1 addition & 2 deletions back-end/pyworkflow/pyworkflow/node_factory.py
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,7 @@


def node_factory(node_info):
# Create a new Node with info
# TODO: should perform error-checking or add default values if missing
"""Create a new Node with info."""
node_type = node_info.get('node_type')
node_key = node_info.get('node_key')

Expand Down
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
from pyworkflow.node import FlowNode, NodeException
from pyworkflow.node import FlowNode
from pyworkflow.parameters import *


class IntegerNode(FlowNode):
"""StringNode object
"""IntegerNode object

Allows for Strings to replace 'string' fields in Nodes
Allows for Integers to replace fields representing numbers in Nodes
"""
name = "Integer Input"
num_in = 0
Expand Down
7 changes: 2 additions & 5 deletions back-end/pyworkflow/pyworkflow/nodes/io/read_csv.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,10 @@


class ReadCsvNode(IONode):
"""ReadCsvNode

Reads a CSV file into a pandas DataFrame.
"""Reads a CSV file into a pandas DataFrame.

Raises:
NodeException: any error reading CSV file, converting
to DataFrame.
NodeException: any error reading CSV file, converting to DataFrame.
"""
name = "Read CSV"
num_in = 0
Expand Down
7 changes: 2 additions & 5 deletions back-end/pyworkflow/pyworkflow/nodes/io/write_csv.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,10 @@


class WriteCsvNode(IONode):
"""WriteCsvNode

Writes the current DataFrame to a CSV file.
"""Writes the current DataFrame to a CSV file.

Raises:
NodeException: any error writing CSV file, converting
from DataFrame.
NodeException: any error writing CSV file, converting from DataFrame.
"""
name = "Write CSV"
num_in = 1
Expand Down
16 changes: 15 additions & 1 deletion back-end/pyworkflow/pyworkflow/nodes/manipulation/filter.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,14 @@


class FilterNode(ManipulationNode):
"""Subset the DataFrame rows or columns according to the specified index labels.

pandas API reference:
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.filter.html

Raises:
NodeException: catches exceptions when dealing with pandas DataFrames.
"""
name = "Filter"
num_in = 1
num_out = 1
Expand All @@ -31,7 +39,13 @@ class FilterNode(ManipulationNode):
def execute(self, predecessor_data, flow_vars):
try:
input_df = pd.DataFrame.from_dict(predecessor_data[0])
output_df = pd.DataFrame.filter(input_df, **self.options)
output_df = pd.DataFrame.filter(
input_df,
items=flow_vars['items'].get_value(),
like=flow_vars['like'].get_value(),
regex=flow_vars['regex'].get_value(),
axis=flow_vars['axis'].get_value(),
)
return output_df.to_json()
except Exception as e:
raise NodeException('filter', str(e))
13 changes: 12 additions & 1 deletion back-end/pyworkflow/pyworkflow/nodes/manipulation/join.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,12 +5,23 @@


class JoinNode(ManipulationNode):
"""Merge DataFrame or named Series objects with a database-style join.

pandas API reference:
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.merge.html

Raises:
NodeException: catches exceptions when dealing with pandas DataFrames.
"""
name = "Joiner"
num_in = 2
num_out = 1

OPTIONS = {
"on": StringParameter("Join Column", docstring="Name of column to join on")
"on": StringParameter(
"Join Column",
docstring="Name of column to join on"
)
}

def execute(self, predecessor_data, flow_vars):
Expand Down
21 changes: 20 additions & 1 deletion back-end/pyworkflow/pyworkflow/nodes/manipulation/pivot.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,14 @@


class PivotNode(ManipulationNode):
"""Create a spreadsheet-style pivot table as a DataFrame.

pandas reference:
https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.pivot_table.html

Raises:
NodeException: catches exceptions when dealing with pandas DataFrames.
"""
name = "Pivoting"
num_in = 1
num_out = 3
Expand Down Expand Up @@ -56,7 +64,18 @@ class PivotNode(ManipulationNode):
def execute(self, predecessor_data, flow_vars):
try:
input_df = pd.DataFrame.from_dict(predecessor_data[0])
output_df = pd.DataFrame.pivot_table(input_df, **self.options)
output_df = pd.DataFrame.pivot_table(
input_df,
index=flow_vars['index'].get_value(),
values=flow_vars['values'].get_value(),
columns=flow_vars['columns'].get_value(),
aggfunc=flow_vars['aggfunc'].get_value(),
fill_value=flow_vars['fill_value'].get_value(),
margins=flow_vars['margins'].get_value(),
dropna=flow_vars['dropna'].get_value(),
margins_name=flow_vars['margins_name'].get_value(),
observed=flow_vars['observed'].get_value(),
)
return output_df.to_json()
except Exception as e:
raise NodeException('pivot', str(e))
9 changes: 5 additions & 4 deletions back-end/pyworkflow/pyworkflow/tests/test_workflow.py
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ def test_workflow_filename(self):

def test_workflow_from_json(self):
new_workflow = Workflow("Untitled", root_dir="/tmp")
workflow_copy = Workflow.from_json(self.workflow.to_session_dict())
workflow_copy = Workflow.from_json(self.workflow.to_json())

self.assertEqual(new_workflow.name, workflow_copy.name)

Expand All @@ -62,16 +62,17 @@ def test_workflow_from_json_key_error(self):
new_workflow = Workflow.from_json(dict())

def test_empty_workflow_to_session(self):
new_workflow = Workflow("Untitled", root_dir="/tmp")
saved_workflow = new_workflow.to_session_dict()
new_workflow = Workflow("Untitled", root_dir="/tmp", node_dir=os.path.join(os.getcwd(), 'nodes'))
saved_workflow = new_workflow.to_json()

workflow_to_compare = {
'name': 'Untitled',
'root_dir': '/tmp',
'node_dir': os.path.join(os.getcwd(), 'nodes'),
'graph': Workflow.to_graph_json(new_workflow.graph),
'flow_vars': Workflow.to_graph_json(new_workflow.flow_vars),
}
self.assertDictEqual(new_workflow.to_session_dict(), workflow_to_compare)
self.assertDictEqual(new_workflow.to_json(), workflow_to_compare)

##########################
# Node lists
Expand Down
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