Merge pull request #4 from RyanStonebraker/dev

Base library refactoring, default interval keys, error checking

mieda/helpers.py

@@ -0,0 +1,142 @@
+"""
+========================================================================================================
+Copyright 2020, by the California Institute of Technology. ALL RIGHTS RESERVED.
+United States Government Sponsorship acknowledged. Any commercial use must be negotiated with the Office of Technology
+Transfer at the California Institute of Technology. This software may be subject to U.S. export control laws. By
+accepting this software, the user agrees to comply with all applicable U.S. export laws and regulations. User has the
+responsibility to obtain export licenses, or other export authority as may be required before exporting such
+information to foreign countries or providing access to foreign persons.
+========================================================================================================
+"""
+
+
+import networkx as nx
+from typing import Union
+
+def createDirectedGraph(intervals: list, key: str) -> nx.DiGraph:
+    # create a directed Graph
+    graph = nx.DiGraph()
+
+    # start by adding the start and ends of the first interval as nodes
+    graph.add_node(intervals[0]["start"])
+    graph.add_node(intervals[0]["finish"])
+
+    # add an edge between the nodes
+    graph.add_edge(
+        **{"u_of_edge": intervals[0]["start"], "v_of_edge": intervals[0]["finish"], key: intervals[0][key]}
+    )
+    return graph
+
+
+def intervalStartsInEndsBefore(graph: nx.DiGraph, pair, interval: dict, key: str):
+    # gather the adjacent attributes
+    left_attrs = set(graph[pair[0]][pair[1]][key])
+    right_attrs = set(interval[key]).union(left_attrs)
+
+    # add edges
+    graph.add_edge(**{"u_of_edge": pair[0], "v_of_edge": interval["start"], key: left_attrs})
+    graph.add_edge(**{"u_of_edge": interval["start"], "v_of_edge": interval["finish"], key: right_attrs})
+    graph.add_edge(**{"u_of_edge": interval["finish"], "v_of_edge": pair[1], key: graph[pair[0]][pair[1]][key]})
+
+    # remove the old edge
+    graph.remove_edge(pair[0], pair[1])
+
+    return graph
+
+
+def intervalStartsInEndsAfter(graph: nx.DiGraph, pair, interval: dict, key: str):
+    # first make an alteration based on the start
+    left_attrs = set(graph[pair[0]][pair[1]][key])
+    right_attrs = set(graph[pair[0]][pair[1]][key]).union(interval[key])
+
+    # add edges
+    graph.add_edge(**{"u_of_edge": pair[0], "v_of_edge": interval["start"], key: left_attrs})
+    graph.add_edge(**{"u_of_edge": interval["start"], "v_of_edge": pair[1], key: right_attrs})
+
+    if pair[1] < interval["finish"]:
+        graph.add_edge(**{"u_of_edge": pair[1], "v_of_edge": interval["finish"], key: interval[key]})
+
+    # remove the old edge
+    graph.remove_edge(pair[0], pair[1])
+
+    return graph
+
+
+def intervalEndsBefore(graph: nx.DiGraph, pair, interval: dict, key: str):
+    # gather the adjacent attributes
+    left_attrs = set(graph[pair[0]][pair[1]][key]).union(interval[key])
+    right_attrs = graph[pair[0]][pair[1]][key]
+
+    # add edges
+    graph.add_edge(**{"u_of_edge": pair[0], "v_of_edge": interval["finish"], key: left_attrs})
+    graph.add_edge(**{"u_of_edge": interval["finish"], "v_of_edge": pair[1], key: right_attrs})
+
+    # remove the old edge
+    graph.remove_edge(pair[0], pair[1])
+
+    return graph
+
+
+def intervalStartsTogether(graph: nx.DiGraph, pair, interval: dict, key: str):
+    interval_split = False
+    # if the current interval ends before
+    if interval["finish"] < pair[1]:
+        graph = intervalEndsBefore(graph, pair, interval, key)
+        interval_split = True
+
+    # if they start at the same time but the current interval ends after
+    if pair[1] < interval["finish"]:
+        # gather the adjacent attributes
+        graph[pair[0]][pair[1]][key] = graph[pair[0]][pair[1]][key].union(
+            interval[key])
+
+        # add edges
+        graph.add_edge(
+            **{"u_of_edge": pair[1], "v_of_edge": interval["finish"], key: interval[key]})
+
+        interval_split = True
+
+    return interval_split, graph
+
+
+def intervalStartsBefore(graph: nx.DiGraph, pair, interval: dict, key: str):
+    interval_split = False
+    # if it ends before
+    if interval["finish"] < pair[1]:
+        # gather the adjacent attributes
+        left_attrs = set(graph[pair[0]][pair[1]][key]).union(
+            interval[key])
+        right_attrs = graph[pair[0]][pair[1]][key]
+
+        # add edges
+        graph.add_edge(
+            **{"u_of_edge": pair[0], "v_of_edge": interval["finish"], key: left_attrs})
+        graph.add_edge(
+            **{"u_of_edge": interval["finish"], "v_of_edge": pair[1], key: right_attrs})
+
+        # remove the old edge
+        graph.remove_edge(pair[0], pair[1])
+
+        interval_split = True
+
+    # if it ends after
+    if pair[1] < interval["finish"]:
+        # gather the adjacent attributes
+        left_attrs = set(graph[pair[0]][pair[1]][key]).union(
+            interval[key])
+        right_attrs = interval[key]
+
+        # add edges
+        graph[pair[0]][pair[1]][key] = left_attrs
+        graph.add_edge(
+            **{"u_of_edge": pair[1], "v_of_edge": interval["finish"], key: right_attrs})
+
+        # remove the old edge
+        try:
+            graph.remove_edge(pair[0], interval["finish"])
+        except nx.NetworkXException:
+            pass
+
+        interval_split = True
+
+    return interval_split, graph