FIX: Restore generate_gantt_chart functionality

.zenodo.json

@@ -788,6 +788,11 @@
     {
       "name": "Tambini, Arielle"
     },
+    {
+      "affiliation": "Child Mind Institute",
+      "name": "Clucas, Jon",
+      "orcid": "0000-0001-7590-5806"
+    },
     {
       "affiliation": "Weill Cornell Medicine",
       "name": "Xie, Xihe",

nipype/pipeline/plugins/tests/test_callback.py

@@ -8,6 +8,13 @@
 import nipype.interfaces.utility as niu
 import nipype.pipeline.engine as pe
 
+try:
+    import pandas
+
+    has_pandas = True
+except ImportError:
+    has_pandas = False
+
 
 def func():
     return
@@ -61,3 +68,38 @@ def test_callback_exception(tmpdir, plugin, stop_on_first_crash):
 
     sleep(0.5)  # Wait for callback to be called (python 2.7)
     assert so.statuses == [("f_node", "start"), ("f_node", "exception")]
+
+
+@pytest.mark.parametrize("plugin", ["Linear", "MultiProc", "LegacyMultiProc"])
+@pytest.mark.skipif(not has_pandas, reason="Test requires pandas")
+def test_callback_gantt(tmpdir, plugin):
+    import logging
+
+    from os import path
+
+    from nipype.utils.profiler import log_nodes_cb
+    from nipype.utils.draw_gantt_chart import generate_gantt_chart
+
+    log_filename = path.join(tmpdir, "callback.log")
+    logger = logging.getLogger("callback")
+    logger.setLevel(logging.DEBUG)
+    handler = logging.FileHandler(log_filename)
+    logger.addHandler(handler)
+
+    # create workflow
+    wf = pe.Workflow(name="test", base_dir=tmpdir.strpath)
+    f_node = pe.Node(
+        niu.Function(function=func, input_names=[], output_names=[]), name="f_node"
+    )
+    wf.add_nodes([f_node])
+    wf.config["execution"] = {"crashdump_dir": wf.base_dir, "poll_sleep_duration": 2}
+
+    plugin_args = {"status_callback": log_nodes_cb}
+    if plugin != "Linear":
+        plugin_args["n_procs"] = 8
+    wf.run(plugin=plugin, plugin_args=plugin_args)
+
+    generate_gantt_chart(
+        path.join(tmpdir, "callback.log"), 1 if plugin == "Linear" else 8
+    )
+    assert path.exists(path.join(tmpdir, "callback.log.html"))

nipype/utils/draw_gantt_chart.py

@@ -12,6 +12,7 @@
 import simplejson as json
 
 from collections import OrderedDict
+from warnings import warn
 
 # Pandas
 try:
@@ -69,9 +70,9 @@ def create_event_dict(start_time, nodes_list):
         finish_delta = (node["finish"] - start_time).total_seconds()
 
         # Populate dictionary
-        if events.get(start_delta) or events.get(finish_delta):
+        if events.get(start_delta):
             err_msg = "Event logged twice or events started at exact same time!"
-            raise KeyError(err_msg)
+            warn(err_msg, category=Warning)
         events[start_delta] = start_node
         events[finish_delta] = finish_node
 
@@ -139,12 +140,18 @@ def calculate_resource_timeseries(events, resource):
     # Iterate through the events
     for _, event in sorted(events.items()):
         if event["event"] == "start":
-            if resource in event and event[resource] != "Unknown":
-                all_res += float(event[resource])
+            if resource in event:
+                try:
+                    all_res += float(event[resource])
+                except ValueError:
+                    continue
             current_time = event["start"]
         elif event["event"] == "finish":
-            if resource in event and event[resource] != "Unknown":
-                all_res -= float(event[resource])
+            if resource in event:
+                try:
+                    all_res -= float(event[resource])
+                except ValueError:
+                    continue
             current_time = event["finish"]
         res[current_time] = all_res
 
@@ -292,7 +299,7 @@ def draw_nodes(start, nodes_list, cores, minute_scale, space_between_minutes, co
             "offset": offset,
             "scale_duration": scale_duration,
             "color": color,
-            "node_name": node["name"],
+            "node_name": node.get("name", node.get("id", "")),
             "node_dur": node["duration"] / 60.0,
             "node_start": node_start.strftime("%Y-%m-%d %H:%M:%S"),
             "node_finish": node_finish.strftime("%Y-%m-%d %H:%M:%S"),
@@ -513,6 +520,23 @@ def generate_gantt_chart(
     # Read in json-log to get list of node dicts
     nodes_list = log_to_dict(logfile)
 
+    # Only include nodes with timing information, and covert timestamps
+    # from strings to datetimes
+    nodes_list = [
+        {
+            k: datetime.datetime.strptime(i[k], "%Y-%m-%dT%H:%M:%S.%f")
+            if k in {"start", "finish"}
+            else i[k]
+            for k in i
+        }
+        for i in nodes_list
+        if "start" in i and "finish" in i
+    ]
+
+    for node in nodes_list:
+        if "duration" not in node:
+            node["duration"] = (node["finish"] - node["start"]).total_seconds()
+
     # Create the header of the report with useful information
     start_node = nodes_list[0]
     last_node = nodes_list[-1]