adding and fixing files #401
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Sequence DiagramsequenceDiagram
participant G as Input Graph
participant CG as Convert to Serializable
participant LP as Generate Layout Positions
participant NC as Assign Node Colors
participant EL as Embed Logo
participant SR as Style and Render
participant OF as Output File
G->>CG: Convert graph
CG->>LP: Compute layout
LP->>NC: Assign colors
NC->>EL: Add logo
EL->>SR: Apply styling
SR->>OF: Render visualization
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Actionable comments posted: 1
🧹 Nitpick comments (7)
cognee/shared/utils.py (7)
15-20: Avoid redundant or overshadowed imports.
These imports duplicate earlier imports (networkx as nxis already defined at line 9, for instance) and can confuse maintainers. Retain them at the top of the file in a single block to improve consistency and readability.- import base64 - import networkx as nx - from bokeh.io import output_file, save - from bokeh.plotting import figure, from_networkx - from bokeh.models import Circle, MultiLine, HoverTool, ColumnDataSource, Range1d + # Remove duplicates or move them to the top unified import section🧰 Tools
🪛 Ruff (0.8.2)
16-16: Redefinition of unused
nxfrom line 9Remove definition:
nx(F811)
228-230: Remove or restore the commented-out code.
This method is commented out entirely. If you no longer needsanitize_df, consider removing it altogether. Otherwise, please restore and maintain relevant tests.
259-269: Duplicate imports repeated here as well.
This block re-imports the same libraries (e.g.,nx,base64) and redefines Bokeh components. Consolidate all imports at the top of the file to follow best practices and eliminate redundancy.- import networkx as nx - from bokeh.plotting import figure, output_file, show - from bokeh.models import Circle, MultiLine, HoverTool, Range1d - from bokeh.io import output_notebook - from bokeh.embed import file_html - from bokeh.resources import CDN - from bokeh.plotting import figure, from_networkx - import base64 - import cairosvg - import logging + # Remove these duplicate imports or merge them into the top block🧰 Tools
🪛 Ruff (0.8.2)
259-259: Module level import not at top of file
(E402)
259-259: Redefinition of unused
nxfrom line 16Remove definition:
nx(F811)
260-260: Module level import not at top of file
(E402)
260-260: Redefinition of unused
figurefrom line 18Remove definition:
figure(F811)
260-260: Redefinition of unused
output_filefrom line 17(F811)
261-261: Module level import not at top of file
(E402)
261-261: Redefinition of unused
Circlefrom line 19Remove definition:
Circle(F811)
261-261: Redefinition of unused
MultiLinefrom line 19Remove definition:
MultiLine(F811)
261-261: Redefinition of unused
HoverToolfrom line 19Remove definition:
HoverTool(F811)
261-261: Redefinition of unused
Range1dfrom line 19Remove definition:
Range1d(F811)
262-262: Module level import not at top of file
(E402)
263-263: Module level import not at top of file
(E402)
264-264: Module level import not at top of file
(E402)
265-265: Module level import not at top of file
(E402)
265-265: Redefinition of unused
figurefrom line 260Remove definition:
figure(F811)
265-265: Redefinition of unused
from_networkxfrom line 18Remove definition:
from_networkx(F811)
266-266: Module level import not at top of file
(E402)
266-266: Redefinition of unused
base64from line 15Remove definition:
base64(F811)
267-267: Module level import not at top of file
(E402)
268-268: Module level import not at top of file
(E402)
270-271: Avoid configuring logging at the library level.
Callinglogging.basicConfighere can override users’ logging settings. Usually, this configuration belongs in the application’s entry point.- logging.basicConfig(level=logging.INFO) + # Remove or relocate this to the application's main entry point or __main__ guard
300-306: Handle missing node attributes gracefully.
This function works as intended. However, if thenode_attributeis missing, nodes default to "Unknown". Consider validating or logging a warning to handle unexpected node data.
308-332: Consider extracting large inline SVG into a separate file.
Storing the logo SVG inline can make maintenance difficult. Keeping the SVG in its own file could reduce clutter and allow quick updates if the logo changes.
436-472: Example usage is helpful; watch for repeated imports.
This section demonstrates the new functions well. However, remove redundant imports that already appear at the top.
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⛔ Files ignored due to path filters (4)
assets/Dashboard_example.pngis excluded by!**/*.pngassets/cognee-logo.pngis excluded by!**/*.pngassets/topoteretes_logo.pngis excluded by!**/*.pngassets/vscode-debug-config.pngis excluded by!**/*.png
📒 Files selected for processing (1)
cognee/shared/utils.py(3 hunks)
🧰 Additional context used
🪛 Ruff (0.8.2)
cognee/shared/utils.py
16-16: Redefinition of unused nx from line 9
Remove definition: nx
(F811)
259-259: Module level import not at top of file
(E402)
259-259: Redefinition of unused nx from line 16
Remove definition: nx
(F811)
260-260: Module level import not at top of file
(E402)
260-260: Redefinition of unused figure from line 18
Remove definition: figure
(F811)
260-260: Redefinition of unused output_file from line 17
(F811)
261-261: Module level import not at top of file
(E402)
261-261: Redefinition of unused Circle from line 19
Remove definition: Circle
(F811)
261-261: Redefinition of unused MultiLine from line 19
Remove definition: MultiLine
(F811)
261-261: Redefinition of unused HoverTool from line 19
Remove definition: HoverTool
(F811)
261-261: Redefinition of unused Range1d from line 19
Remove definition: Range1d
(F811)
262-262: Module level import not at top of file
(E402)
263-263: Module level import not at top of file
(E402)
264-264: Module level import not at top of file
(E402)
265-265: Module level import not at top of file
(E402)
265-265: Redefinition of unused figure from line 260
Remove definition: figure
(F811)
265-265: Redefinition of unused from_networkx from line 18
Remove definition: from_networkx
(F811)
266-266: Module level import not at top of file
(E402)
266-266: Redefinition of unused base64 from line 15
Remove definition: base64
(F811)
267-267: Module level import not at top of file
(E402)
268-268: Module level import not at top of file
(E402)
🔇 Additional comments (4)
cognee/shared/utils.py (4)
293-298: Layout generation looks solid.
This code appropriately uses the provided layout function and returns a scaled dictionary of positions.
333-355: Styling logic is well-structured.
The usage of from_networkx and node radius calculations are clear. This approach is well-suited for Bokeh visualizations.
422-431: graph_to_tuple implementation looks appropriate.
It collects nodes and edges with attributes into lists. This approach is straightforward for serialization or partial transformations.
356-420: Combine tasks successfully; verify the fixed convert_to_serializable_graph.
The overall flow is good, but it depends on the correction of the logic bug in convert_to_serializable_graph. After fixing, ensure this function produces the intended result.
| def convert_to_serializable_graph(G): | ||
| """ | ||
| Convert a graph into a serializable format with stringified node and edge attributes. | ||
| """ | ||
|
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||
| # Perform Named Entity Recognition (NER) on the tagged tokens | ||
| entities = get_entities(tagged_tokens) | ||
| (nodes, edges) = G | ||
| networkx_graph = nx.MultiDiGraph() | ||
|
|
||
| return entities | ||
| networkx_graph.add_nodes_from(nodes) | ||
| networkx_graph.add_edges_from(edges) | ||
|
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||
| new_G = nx.MultiDiGraph() if isinstance(G, nx.MultiDiGraph) else nx.Graph() | ||
| print(new_G) | ||
| for node, data in new_G.nodes(data=True): | ||
| serializable_data = {k: str(v) for k, v in data.items()} | ||
| new_G.add_node(str(node), **serializable_data) | ||
| for u, v, data in new_G.edges(data=True): | ||
| serializable_data = {k: str(v) for k, v in data.items()} | ||
| new_G.add_edge(str(u), str(v), **serializable_data) | ||
| return new_G |
There was a problem hiding this comment.
Incorrect logic in convert_to_serializable_graph.
The code never transfers nodes/edges from networkx_graph into new_G. Iterating over new_G while it’s empty prevents any data from being copied.
Below is a sample fix ensuring new_G is properly populated:
def convert_to_serializable_graph(G):
(nodes, edges) = G
- networkx_graph = nx.MultiDiGraph()
+ networkx_graph = nx.MultiDiGraph() if isinstance(G, nx.MultiDiGraph) else nx.Graph()
networkx_graph.add_nodes_from(nodes)
networkx_graph.add_edges_from(edges)
- new_G = nx.MultiDiGraph() if isinstance(G, nx.MultiDiGraph) else nx.Graph()
- print(new_G)
- for node, data in new_G.nodes(data=True):
+ new_G = nx.MultiDiGraph() if isinstance(networkx_graph, nx.MultiDiGraph) else nx.Graph()
+ for node, data in networkx_graph.nodes(data=True):
serializable_data = {k: str(v) for k, v in data.items()}
new_G.add_node(str(node), **serializable_data)
- for u, v, data in new_G.edges(data=True):
+ for u, v, edge_data in networkx_graph.edges(data=True):
serializable_data = {k: str(val) for k, val in edge_data.items()}
new_G.add_edge(str(u), str(v), **serializable_data)
return new_G📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| def convert_to_serializable_graph(G): | |
| """ | |
| Convert a graph into a serializable format with stringified node and edge attributes. | |
| """ | |
| # Perform Named Entity Recognition (NER) on the tagged tokens | |
| entities = get_entities(tagged_tokens) | |
| (nodes, edges) = G | |
| networkx_graph = nx.MultiDiGraph() | |
| return entities | |
| networkx_graph.add_nodes_from(nodes) | |
| networkx_graph.add_edges_from(edges) | |
| new_G = nx.MultiDiGraph() if isinstance(G, nx.MultiDiGraph) else nx.Graph() | |
| print(new_G) | |
| for node, data in new_G.nodes(data=True): | |
| serializable_data = {k: str(v) for k, v in data.items()} | |
| new_G.add_node(str(node), **serializable_data) | |
| for u, v, data in new_G.edges(data=True): | |
| serializable_data = {k: str(v) for k, v in data.items()} | |
| new_G.add_edge(str(u), str(v), **serializable_data) | |
| return new_G | |
| def convert_to_serializable_graph(G): | |
| """ | |
| Convert a graph into a serializable format with stringified node and edge attributes. | |
| """ | |
| (nodes, edges) = G | |
| networkx_graph = nx.MultiDiGraph() if isinstance(G, nx.MultiDiGraph) else nx.Graph() | |
| networkx_graph.add_nodes_from(nodes) | |
| networkx_graph.add_edges_from(edges) | |
| new_G = nx.MultiDiGraph() if isinstance(networkx_graph, nx.MultiDiGraph) else nx.Graph() | |
| for node, data in networkx_graph.nodes(data=True): | |
| serializable_data = {k: str(v) for k, v in data.items()} | |
| new_G.add_node(str(node), **serializable_data) | |
| for u, v, edge_data in networkx_graph.edges(data=True): | |
| serializable_data = {k: str(val) for k, val in edge_data.items()} | |
| new_G.add_edge(str(u), str(v), **serializable_data) | |
| return new_G |
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