Merge pull request #18 from neuronsimulator/olupton/tasty-fudge

model-specific output fudging + generic patterns.

Author: nrnhines

modeldb/modeldb-run.yaml

@@ -62,6 +62,9 @@
     - run()
     - verify_graph_()
 3434:
+    curate_patterns:
+      - pattern: 'realtime = [0-9]+\.[0-9]+ s'
+        repl: 'realtime = %wallclock_time%'
     run:
     - init()
     - gr.showAllTimeGraphs=1
@@ -1011,6 +1014,16 @@
     run:
     - ParmFitnessGui[0].run()
     - verify_graph_()
+146030:
+    curate_patterns:
+      - pattern: 'Setup time for simulation: [0-9]+\.[0-9]+  seconds'
+        repl: 'Setup time for simulation: %setup_time% seconds'
+      - pattern: 'Starting simulation of duration 300\.0 ms, dt: 0\.025, reference: Sim_8c at time: \d+/\d+/\d+,\d+:\d+:\d+ [AP]{1}M:\d+'
+        repl: 'Starting simulation of duration 300\.0 ms, dt: 0\.025, reference: Sim_8c at time: %current_date%'
+      - pattern: 'Finished simulation in [0-9]+\.[0-9]+ seconds'
+        repl: 'Finished simulation in %simulation_time% seconds'
+      - pattern: 'Current time: \d+/\d+/\d+,\d+:\d+:\d+ [AP]{1}M:\d+'
+        repl: 'Current time: %current_time%'
 147461:
     comment: //do not run Minimum time would be 1/2 hr default time is about 8.3 hours
     run: null
@@ -1019,6 +1032,9 @@
     - demo_run()
     - verify_graph_()
 150245:
+    curate_patterns:
+      - pattern: 't=100\.00;122\([0-9]+\.[0-9]+\)'
+        repl: 't=100.00;122(%some_kind_of_clock%)'
     run:
     - tstop=100
     - init()
@@ -1031,6 +1047,12 @@
     comment: //do not run Tried "initDialog.unmap(1)" - didnt work.  Need to change
         archive
     run: null
+187604:
+  curate_patterns:
+    - pattern: 'TIME HOST 0: [0-9\.]+ seconds \(set up\)'
+      repl: 'TIME HOST 0: %elapsed_time% seconds (set up)'
+    - pattern: 'TIME HOST 0: [0-9\.]+ seconds \(created cells\)'
+      repl: 'TIME HOST 0: %elapsed_time% seconds (created cells)'
 206244:
     run:
     - chdir("mechanism")

modeldb/report.py

@@ -2,14 +2,17 @@
 import json
 import re
 import difflib
+import logging
 import os
 import subprocess
+from .modeldb import ModelDB
 from pygments import highlight
 from pygments.lexers import DiffLexer
 from pygments.formatters import HtmlFormatter
 
+mdb = ModelDB()
 
-def curate_run_data(run_data):
+def curate_run_data(run_data, model=None):
     curated_data = run_data
 
     regex_dict = {
@@ -19,10 +22,22 @@ def curate_run_data(run_data):
         # nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed" <-> special: unableto open font "*helvetica-medium-r-normal*--14*", using "fixed"
         "^nrniv:": "%neuron-executable%:",
         "^special:": "%neuron-executable%:",
+        "(Mon|Tue|Wed|Thu|Fri|Sat|Sun) (Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec) \d+ \d+:\d+:\d+ [A-Z]+ \d+": "%date_command%",
+        "total run time [0-9\.]+": "total run time %run_time%",
     }
 
+    for model_specific_substitution in mdb.run_instr.get(model, {}).get("curate_patterns", []):
+        regex_dict[model_specific_substitution["pattern"]] = model_specific_substitution["repl"]
+
     for regex_key, regex_value in regex_dict.items():
-        curated_data = [re.sub(regex_key, regex_value, line) for line in curated_data]
+        updated_data = []
+        for line in curated_data:
+            new_line, number_of_subs = re.subn(regex_key, regex_value, line)
+            if number_of_subs:
+                logging.debug("{} matched {} time(s)".format(regex_key, number_of_subs))
+                logging.debug("{} -> {}".format(line, new_line))
+            updated_data.append(new_line)
+        curated_data = updated_data
 
     return curated_data
 
@@ -41,8 +56,8 @@ def diff_reports(report1_json, report2_json):
         for k in data_a.keys():
             if int(k) == 0:
                 continue  # skip info key
-            curated_a = curate_run_data(data_a[k]["nrn_run"])
-            curated_b = curate_run_data(data_b[k]["nrn_run"])
+            curated_a = curate_run_data(data_a[k]["nrn_run"], model=int(k))
+            curated_b = curate_run_data(data_b[k]["nrn_run"], model=int(k))
             if curated_a != curated_b:
                 diff_dict[k] = hd.make_table(curated_a, curated_b, context=True).replace("\n", " ")
             if "do_not_run" not in data_a[k]: