From 2263bac208ce7f73f5de422b90ecb6761f28abe5 Mon Sep 17 00:00:00 2001
From: Olga Ivanova <ivanovaos.09@gmail.com>
Date: Wed, 3 Jul 2024 15:24:20 +0200
Subject: [PATCH] removing mock network obj from visuals

---
 networkcommons/_visual/_network_mock.py | 102 ------------------------
 1 file changed, 102 deletions(-)
 delete mode 100644 networkcommons/_visual/_network_mock.py

diff --git a/networkcommons/_visual/_network_mock.py b/networkcommons/_visual/_network_mock.py
deleted file mode 100644
index a14f3a0..0000000
--- a/networkcommons/_visual/_network_mock.py
+++ /dev/null
@@ -1,102 +0,0 @@
-from typing import Dict, List
-import networkx as nx
-import pandas as pd
-from pypath.utils import mapping
-
-import vis_yfiles
-import vis_networkx
-
-
-class NetworkMock:
-
-    def __init__(self):
-        self.network = nx.DiGraph()
-        self.color_map = {}
-
-    def init_from_sif(self, filepath):
-        """
-        Initialize the network from a SIF file
-        """
-        with open(filepath, 'r') as f:
-            for line in f:
-                source, effect, target = line.strip().split()
-                self.network.add_edge(source, target)
-                self.update_edge_property((source, target), type="effect", value=effect)
-
-
-        return self.network
-
-    def add_nodes(self, nodes):
-        self.network.add_nodes_from(nodes)
-        return self.network
-
-    def set_source_nodes(self, source_nodes):
-        self.update_node_property(source_nodes, type="source", value="1")
-
-    def set_target_nodes(self, target_nodes):
-        self.update_node_property(target_nodes, type="target", value="1")
-
-    def set_nodes_of_interest(self, nodes):
-        self.update_node_property(nodes, type="noi", value="1")
-
-    def add_edges(self, edges):
-        self.network.add_edges_from(edges)
-
-    def update_node_property(self, node, type="color", value="blue"):
-        # add color to the node in networkx
-        if type == "color":
-            self.color_map[node] = value
-        elif type == "initial_node":
-            self.network.nodes[node]["initial_node"] = True
-        return self.color_map
-
-    def update_edge_property(self, edge, type="color", value="blue"):
-        # add color to the edge in networkx
-        if type == "color":
-            self.color_map[edge] = value
-        elif type == "effect":
-            self.network.edges[edge]["effect"] = value
-        else:
-            raise ValueError("Invalid edge property")
-        return self.color_map
-
-    def visualise(self, filepath=None, render=False, visualiser="networkx"):
-        if visualiser == "yfiles":
-            yfiles_vis = vis_yfiles.YFilesVisualizer(self.network)
-            yfiles_vis.visualise(graph_layout="hierarchical", directed=True)
-        elif visualiser == "networkx":
-            networkx_vis = vis_networkx.NetworkXVisualizer(self.network)
-            networkx_vis.visualise(render=render)
-        else:
-            raise ValueError("Invalid visualiser")
-
-    def mapping_node_identifier(self, node: str) -> List[str]:
-        complex_string = None
-        gene_symbol = None
-        uniprot = None
-
-        if mapping.id_from_label0(node):
-            uniprot = mapping.id_from_label0(node)
-            gene_symbol = mapping.label(uniprot)
-        elif node.startswith("COMPLEX"):
-            node = node[8:] #TODO change to wrap
-            node_list = node.split("_")
-            translated_node_list = [mapping.label(mapping.id_from_label0(item)) for item in node_list]
-            complex_string = "COMPLEX:" + "_".join(translated_node_list)
-        elif mapping.label(node):
-            gene_symbol = mapping.label(node)
-            uniprot = mapping.id_from_label0(gene_symbol)
-        else:
-            print("Error during translation, check syntax for ", node)
-
-        return [complex_string, gene_symbol, uniprot]
-
-    def convert_edges_into_genesymbol(self, edges: pd.DataFrame) -> pd.DataFrame:
-        def convert_identifier(x):
-            identifiers = self.mapping_node_identifier(x)
-            return identifiers[1]  # Using GeneSymbol
-        edges["source"] = edges["source"].apply(convert_identifier)
-        edges["target"] = edges["target"].apply(convert_identifier)
-        return edges
-
-