Store pipeline state + switch to argparse

The raw data and the analysis results do not constitute the entire state of a
pipeline. In particular, if we store only the raw + analysis results, and then
we try to run the pipeline again, we will end up with two copies of the
analysis results.

Instead, when we transfer data, it should include the raw data, the pipeline
state, and the analysis results.

Change this code to store the pipeline state as well.

And since I am in there changing things anyway, switch to argparse to handle
the arguments as well.

```
$ ./e-mission-py.bash bin/debug/extract_timeline_for_day_range_and_user.py -e test_output_gen_curr_ts -- 2010-01-01 2020-01-01 /tmp/test_dump
storage not configured, falling back to sample, default configuration
Connecting to database URL localhost
INFO:root:==================================================
INFO:root:Extracting timeline for user d4dfcc42-b6fc-4b6b-a246-d1abec1d039f day 2010-01-01 -> 2020-01-01 and saving to file /tmp/test_dump
DEBUG:root:start_day_ts = 1262304000 (2010-01-01T00:00:00+00:00), end_day_ts = 1577836800 (2020-01-01T00:00:00+00:00)
DEBUG:root:curr_query = {'user_id': UUID('d4dfcc42-b6fc-4b6b-a246-d1abec1d039f'), 'data.ts': {'$lte': 1577836800, '$gte': 1262304000}}, sort_key = data.ts
DEBUG:root:orig_ts_db_keys = None, analysis_ts_db_keys = None
DEBUG:root:finished querying values for None
DEBUG:root:finished querying values for None
DEBUG:root:curr_query = {'user_id': UUID('d4dfcc42-b6fc-4b6b-a246-d1abec1d039f'), 'data.start_ts': {'$lte': 1577836800, '$gte': 1262304000}}, sort_key = data.start_ts
DEBUG:root:orig_ts_db_keys = None, analysis_ts_db_keys = None
DEBUG:root:finished querying values for None
DEBUG:root:finished querying values for None
DEBUG:root:curr_query = {'user_id': UUID('d4dfcc42-b6fc-4b6b-a246-d1abec1d039f'), 'data.enter_ts': {'$lte': 1577836800, '$gte': 1262304000}}, sort_key = data.enter_ts
DEBUG:root:orig_ts_db_keys = None, analysis_ts_db_keys = None
DEBUG:root:finished querying values for None
DEBUG:root:finished querying values for None
INFO:root:Found 1449 loc entries, 27 trip-like entries, 19 place-like entries = 1495 total entries
INFO:root:timeline has unique keys = {'stats/server_api_error', 'statemachine/transition', 'analysis/cleaned_stop', 'background/filtered_location', 'segmentation/raw_trip', 'background/location', 'segmentation/raw_stop', 'segmentation/raw_section', 'stats/client_time', 'background/motion_activity', 'analysis/recreated_location', 'segmentation/raw_place', 'analysis/cleaned_trip', 'background/battery', 'analysis/cleaned_section', 'stats/server_api_time', 'analysis/cleaned_place', 'stats/pipeline_time', 'stats/client_nav_event'}
INFO:root:Found 6 pipeline states [6, 1, 2, 3, 11, 9]

$ ls -1 /tmp/test_dump_*
/tmp/test_dump_d4dfcc42-b6fc-4b6b-a246-d1abec1d039f.gz
/tmp/test_dump_pipelinestate_d4dfcc42-b6fc-4b6b-a246-d1abec1d039f.gz
```

bin/debug/extract_timeline_for_day_range_and_user.py

@@ -19,6 +19,7 @@
 import arrow
 import argparse
 
+import emission.core.wrapper.user as ecwu
 import emission.storage.timeseries.abstract_timeseries as esta
 import emission.storage.timeseries.timequery as estt
 import emission.storage.decorations.user_queries as esdu
@@ -53,9 +54,25 @@ def export_timeline(user_id, start_day_str, end_day_str, file_name):
     if len(combined_list) == 0 or unique_key_list == set(['stats/pipeline_time']):
         logging.info("No entries found in range for user %s, skipping save" % user_id)
     else:
+        # Also dump the pipeline state, since that's where we have analysis results upto
+        # This allows us to copy data to a different *live system*, not just
+        # duplicate for analysis
         combined_filename = "%s_%s.gz" % (file_name, user_id)
-        json.dump(combined_list,
-            gzip.open(combined_filename, "wb"), default=bju.default, allow_nan=False, indent=4)
+        with gzip.open(combined_filename, "wt") as gcfd:
+            json.dump(combined_list,
+                gcfd, default=bju.default, allow_nan=False, indent=4)
+
+        import emission.core.get_database as edb
+
+        pipeline_state_list = list(edb.get_pipeline_state_db().find({"user_id": user_id}))
+        logging.info("Found %d pipeline states %s" %
+            (len(pipeline_state_list),
+             list([ps["pipeline_stage"] for ps in pipeline_state_list])))
+
+        pipeline_filename = "%s_pipelinestate_%s.gz" % (file_name, user_id)
+        with gzip.open(pipeline_filename, "wt") as gpfd:
+            json.dump(pipeline_state_list,
+                gpfd, default=bju.default, allow_nan=False, indent=4)
 
 def validate_truncation(loc_entry_list, trip_entry_list, place_entry_list):
     MAX_LIMIT = 25 * 10000
@@ -70,20 +87,33 @@ def export_timeline_for_users(user_id_list, args):
     for curr_uuid in user_id_list:
         if curr_uuid != '':
             logging.info("=" * 50)
-            export_timeline(user_id=curr_uuid, start_day_str=sys.argv[2], end_day_str=sys.argv[3], file_name=sys.argv[4])
-
+            export_timeline(user_id=curr_uuid, start_day_str=args.start_day,
+                end_day_str= args.end_day, file_name=args.file_prefix)
 
 if __name__ == '__main__':
-    if len(sys.argv) != 5:
-        print("Usage: %s [<user>|'all'|'file_XXX'] <start_day> <end_day> <file_prefix>" % (sys.argv[0]))
-    else:
-        user_id_str = sys.argv[1]
-        if user_id_str == "all":
-            all_uuids = esdu.get_all_uuids()
-            export_timeline_for_users(all_uuids, sys.argv)
-        elif user_id_str.startswith("file_"):
-            uuid_strs = json.load(open(user_id_str))
-            uuids = [uuid.UUID(ustr) for ustr in uuid_strs]
-            export_timeline_for_users(uuids, sys.argv)
-        else:
-            export_timeline(user_id=uuid.UUID(sys.argv[1]), start_day_str=sys.argv[2], end_day_str=sys.argv[3], file_name=sys.argv[4])
+    logging.basicConfig(level=logging.DEBUG)
+    parser = argparse.ArgumentParser(prog="extract_timeline_for_day_range_and_user")
+
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument("-e", "--user_email", nargs="+")
+    group.add_argument("-u", "--user_uuid", nargs="+")
+    group.add_argument("-a", "--all", action="store_true")
+    group.add_argument("-f", "--file")
+
+    parser.add_argument("start_day", help="start day in utc - e.g. 'YYYY-MM-DD'" )
+    parser.add_argument("end_day", help="start day in utc - e.g. 'YYYY-MM-DD'" )
+    parser.add_argument("file_prefix", help="prefix for the filenames generated - e.g /tmp/dump_ will generate files /tmp/dump_<uuid1>.gz, /tmp/dump_<uuid2>.gz..." )
+
+    args = parser.parse_args()
+
+    if args.user_uuid:
+        uuid_list = [uuid.UUID(uuid_str) for uuid_str in args.user_uuid]
+    elif args.user_email:
+        uuid_list = [ecwu.User.fromEmail(uuid_str).uuid for uuid_str in args.user_email]
+    elif args.all:
+        uuid_list = esdu.get_all_uuids()
+    elif args.file:
+        with open(args.file) as fd:
+            uuid_strs = json.load(fd)
+            uuid_list = [uuid.UUID(ustr) for ustr in uuid_strs]
+    export_timeline_for_users(uuid_list, args)