Merge pull request #29 from loudnate/dev

Next version (dev)

README.md

@@ -26,26 +26,26 @@ $ python setup.py develop
 ### Adding to your openaps project
 ```bash
 $ openaps vendor add openapscontrib.mmhistorytools
-$ openaps device add munge mmhistorytools
+$ openaps device add history mmhistorytools
 ```
 
 ## Usage
 Use the device help menu to see available commands.
 ```bash
-$ openaps use munge -h
-usage: openaps-use munge [-h] USAGE ...
+$ openaps use history -h
+usage: openaps-use history [-h] USAGE ...
 
 optional arguments:
   -h, --help  show this help message and exit
 
-## Device munge:
+## Device history:
   vendor openapscontrib.mmhistorytools
-  
+
   mmhistorytools - tools for cleaning, condensing, and reformatting history data
-  
-  
-  
-      
+
+
+
+
 
   USAGE       Usage Details
     trim      Trims a sequence of pump history to a specified time window
@@ -61,8 +61,8 @@ optional arguments:
 
 Use the command help menu to see available arguments.
 ```bash
-$ openaps use munge clean -h
-usage: openaps-use munge clean [-h] [--start START] [--end END] [infile]
+$ openaps use history clean -h
+usage: openaps-use history clean [-h] [--start START] [--end END] [infile]
 
 Resolve inconsistencies from a sequence of pump history
 
@@ -85,24 +85,24 @@ Tasks performed by this pass:
 
 Add a report flow to process pump history for analysis:
 ```
-$ openaps report add clean_history.json JSON munge clean pump_history.json
-$ openaps report add reconciled_history.json JSON munge reconcile clean_history.json
-$ openaps report add resolved_history.json JSON munge resolve reconciled_history.json
-$ openaps report add normalized_history.json JSON munge normalize resolved_history.json --basal-profile basal.json --zero-at read_clock.json
+$ openaps report add clean_history.json JSON history clean pump_history.json
+$ openaps report add reconciled_history.json JSON history reconcile clean_history.json
+$ openaps report add resolved_history.json JSON history resolve reconciled_history.json
+$ openaps report add normalized_history.json JSON history normalize resolved_history.json --basal-profile basal.json --zero-at read_clock.json
 ```
 
 All `infile` arguments default to accept stdin, so commands can be chained to simplify testing:
 ```bash
-$ openaps use pump iter_pump_hours 4 | openaps use munge clean | openaps use munge reconcile | openaps use munge resolve | openaps use munge normalize --basal-profile basal.json --zero-at read_clock.json
+$ openaps use pump iter_pump_hours 4 | openaps use history clean | openaps use history reconcile | openaps use history resolve | openaps use history normalize --basal-profile basal.json --zero-at read_clock.json
 ```
 
 ## Contributing
 Contributions are welcome and encouraged in the form of bugs and pull requests.
 
 ### Testing
- 
+
  Unit tests can be run manually via setuptools. This is also handled by TravisCI after opening a pull request.
- 
+
  ```bash
  $ python setup.py test
  ```

openapscontrib/mmhistorytools/__init__.py

@@ -13,6 +13,7 @@
 
 from historytools import TrimHistory, CleanHistory, ReconcileHistory
 from historytools import ResolveHistory, NormalizeRecords
+from historytools import AppendDoseToHistory
 
 
 # set_config is needed by openaps for all vendors.
@@ -38,7 +39,7 @@ def display_device(device):
 # agp as a vendor.  Return a list of classes which inherit from Use,
 # or are compatible with it:
 def get_uses(device, config):
-    return [trim, clean, reconcile, resolve, normalize]
+    return [trim, clean, reconcile, resolve, normalize, append_dose, prepare]
 
 
 def _opt_date(timestamp):
@@ -215,13 +216,17 @@ class resolve(BaseUse):
 - `Bolus`: Insulin delivery events in Units, or Units/hour
 - `Meal`: Grams of carbohydrate
 - `TempBasal`: Paced insulin delivery events in Units/hour, or Percent of scheduled basal
+- `Exercise`: Exercise event
+_
 The following history events are parsed:
 - TempBasal and TempBasalDuration are combined into TempBasal records
 - PumpSuspend and PumpResume are combined into TempBasal records of 0%
 - Square Bolus is converted to a Bolus record
 - Normal Bolus is converted to a Bolus record
 - BolusWizard carb entry is converted to a Meal record
 - JournalEntryMealMarker is converted to a Meal record
+- JournalEntryExerciseMarker is converted to an Exercise record
+_
 Events that are not related to the record types or seem to have no effect are dropped.
 """
     def main(self, args, app):
@@ -239,6 +244,7 @@ class normalize(BaseUse):
 If `--basal-profile` is provided, the TempBasal `amount` is replaced with a relative dose in
 Units/hour. A single TempBasal record might split into multiple records to account for boundary
 crossings in the basal schedule.
+_
 If `--zero-at` is provided, the values for the `start_at` and `end_at` keys are replaced with signed
 integers representing the number of minutes from `--zero-at`.
 """
@@ -291,3 +297,91 @@ def main(self, args, app):
         tool = NormalizeRecords(*args, **kwargs)
 
         return tool.normalized_records
+
+
+# noinspection PyPep8Naming
+class append_dose(BaseUse):
+    """Appends a dose record to a sequence of cleaned history
+
+The expected dose record format is a dictionary with a key named "recieved" (sic).
+If that key isn't present, or its value is false, the record is ignored.
+"""
+
+    def configure_app(self, app, parser):
+        super(append_dose, self).configure_app(app, parser)
+
+        parser.add_argument(
+            '--dose',
+            help='JSON-encoded dosing report'
+        )
+
+    def get_params(self, args):
+        params = super(append_dose, self).get_params(args)
+
+        params.update(dose=args.dose)
+
+        return params
+
+    def get_program(self, params):
+        args, kwargs = super(append_dose, self).get_program(params)
+
+        args.append(_opt_json_file(params['dose']))
+
+        return args, kwargs
+
+    def main(self, args, app):
+        args, _ = self.get_program(self.get_params(args))
+
+        tool = AppendDoseToHistory(*args)
+
+        return tool.appended_history
+
+
+# noinspection PyPep8Naming
+class prepare(BaseUse):
+    """Runs a sequence of commands to prepare history for use in prediction and dosing.
+
+This command performs the following commands in sequence:
+[clean] -> [reconcile] -> [resolve] -> [normalize:basal-profile]
+_
+Please refer to the --help documentation of each command for more information.
+_
+Warning: This command will not return the same level of diagnostic logging as
+running all four commands separately. If there is reason to believe an issue
+has occurred, output from this command may not be sufficient for debugging.
+"""
+
+    def configure_app(self, app, parser):
+        super(prepare, self).configure_app(app, parser)
+
+        parser.add_argument(
+            '--basal-profile',
+            default=None,
+            help='A file containing a basal profile by which to adjust TempBasal records'
+        )
+
+    def get_params(self, args):
+        params = super(prepare, self).get_params(args)
+        if 'basal_profile' in args and args.basal_profile:
+            params.update(basal_profile=args.basal_profile)
+
+        return params
+
+    def get_program(self, params):
+        args, kwargs = super(prepare, self).get_program(params)
+
+        kwargs.update(
+            basal_schedule=_opt_json_file(params.get('basal_profile'))
+        )
+
+        return args, kwargs
+
+    def main(self, args, app):
+        args, kwargs = self.get_program(self.get_params(args))
+
+        clean_history = CleanHistory(*args).clean_history
+        reconciled_history = ReconcileHistory(clean_history).reconciled_history
+        resolved_records = ResolveHistory(reconciled_history).resolved_records
+        normalized_records = NormalizeRecords(resolved_records, **kwargs).normalized_records
+
+        return normalized_records

openapscontrib/mmhistorytools/historytools.py

@@ -4,7 +4,7 @@
 from datetime import timedelta
 from dateutil import parser
 
-from .models import Bolus, Meal, TempBasal, Unit
+from .models import Bolus, Meal, TempBasal, Exercise, Unit
 
 
 class ParseHistory(object):
@@ -254,6 +254,7 @@ class ResolveHistory(ParseHistory):
     - `Bolus`: Insulin delivery events in Units, or Units/hour
     - `Meal`: Grams of carbohydrate
     - `TempBasal`: Paced insulin delivery events in Units/hour, or Percent of scheduled basal
+    - `Exercise`: Exercise event
 
     The following history events are parsed:
 
@@ -263,6 +264,7 @@ class ResolveHistory(ParseHistory):
     - Normal Bolus is converted to a Bolus record
     - BolusWizard carb entry is converted to a Meal record
     - JournalEntryMealMarker is converted to a Meal record
+    - JournalEntryExerciseMarker is converted to an Exercise record
 
     Events that are not related to the record types or seem to have no effect are dropped.
     """
@@ -345,6 +347,18 @@ def _decode_journalentrymealmarker(self, event):
                 description='{}: {}g'.format(event["_type"], carb_input)
             )
 
+    def _decode_journalentryexercisemarker(self, event):
+        num_events = 1
+        start_at = self._event_datetime(event)
+
+        return Exercise(
+            start_at=start_at,
+            end_at=start_at,
+            amount=num_events,
+            unit=Unit.event,
+            description=event["_type"]
+        )
+
     def _decode_pumpresume(self, event):
         self._resume_datetime = self._event_datetime(event)
 
@@ -569,3 +583,46 @@ def _decode_tempbasal(self, event):
                 )
 
                 return events
+
+
+class AppendDoseToHistory(ParseHistory):
+    """Append a dose record or records to a list of history records.
+
+    The expected dose record format is a dictionary with a key named "recieved" (sic).
+    If that key isn't present, or its value is false, the record is ignored.
+    """
+    def __init__(self, clean_history, doses):
+        """Initializes a new instance of the history parser
+
+        :param clean_history: A list of pump history events in reverse-chronological order
+        :type clean_history: list(dict)
+        :param doses: A single dose event, or a list of dose events in chronological order
+        :type doses: list(dict)|dict
+        """
+        self.appended_history = clean_history
+
+        if isinstance(doses, dict):
+            doses = [doses]
+
+        for event in doses:
+            if event.get('recieved', False) is True:
+                self.add_history_event(event)
+
+    def add_history_event(self, event):
+        try:
+            decoded = getattr(self, '_decode_{}'.format(event['type'].lower()))(event)
+        except AttributeError:
+            decoded = [event]
+
+        for decoded_event in decoded:
+            self.appended_history.insert(0, decoded_event)
+
+    def _decode_tempbasal(self, event):
+        amount_event = copy(event)
+        amount_event['_type'] = amount_event.pop('type')
+
+        duration_event = copy(event)
+        duration_event['_type'] = '{}Duration'.format(duration_event.pop('type'))
+        duration_event[self.DURATION_IN_MINUTES_KEY] = duration_event.pop('duration')
+
+        return [amount_event, duration_event]

openapscontrib/mmhistorytools/models.py

@@ -41,11 +41,16 @@ class TempBasal(BaseRecord):
     pass
 
 
+class Exercise(BaseRecord):
+    pass
+
+
 class Unit(object):
     grams = "g"
     percent_of_basal = "percent"
     units = "U"
     units_per_hour = "U/hour"
+    event = "event"
 
 
 class RecordJSONEncoder(json.JSONEncoder):

openapscontrib/mmhistorytools/version.py

@@ -1 +1 @@
-__version__ = '0.0.4'
+__version__ = '0.1.0'

tests/fixtures/exercise_marker.json

@@ -0,0 +1,10 @@
+[
+  {
+    "_type": "JournalEntryExerciseMarker", 
+    "_description": "JournalEntryExerciseMarker 2015-09-07T15:38:23 head[2], body[1] op[0x41]", 
+    "timestamp": "2015-09-07T15:38:23", 
+    "_body": "00", 
+    "_head": "4100", 
+    "_date": "97660f070f"
+  }
+]

tests/fixtures/set_dose.json

@@ -0,0 +1,10 @@
+[
+  {
+    "temp": "absolute",
+    "recieved": true,
+    "rate": 1.425,
+    "timestamp": "2015-09-19T20:25:27.468623",
+    "duration": 30,
+    "type": "TempBasal"
+  }
+]

tests/fixtures/set_two_doses.json

@@ -0,0 +1,18 @@
+[
+  {
+    "temp": "percent",
+    "recieved": true,
+    "rate": 100,
+    "timestamp": "2015-07-27T16:45:29.737754",
+    "duration": 0,
+    "type": "TempBasal"
+  },
+  {
+    "temp": "percent",
+    "recieved": true,
+    "rate": 140,
+    "timestamp": "2015-07-27T16:45:31.320183",
+    "duration": 30,
+    "type": "TempBasal"
+  }
+]