feat: use delphi-logger

* update requirements files to use git repo
* import logger from delphi-logger package instead of relative
* remove duplicate logger.py in this repo
* update delphi-epidata.py client to only depend on logger

Author: dshemetov

requirements.api.txt

@@ -1,4 +1,5 @@
 delphi_utils
+delphi_logger @ git+https://github.com/cmu-delphi/delphi-logger
 epiweeks==2.1.2
 Flask==2.2.5
 Flask-Limiter==3.3.0

requirements.dev.txt

@@ -3,6 +3,7 @@ black>=20.8b1
 bump2version==1.0.1
 covidcast==0.1.5
 delphi_utils
+delphi_logger @ git+https://github.com/cmu-delphi/delphi-logger
 docker==6.0.1
 dropbox==11.36.0
 freezegun==1.2.2

src/acquisition/covid_hosp/common/database.py

@@ -11,7 +11,7 @@
 
 # first party
 import delphi.operations.secrets as secrets
-from delphi.epidata.common.logger import get_structured_logger
+from delphi_logger import get_structured_logger
 
 Columndef = namedtuple("Columndef", "csv_name sql_name dtype")
 

src/acquisition/covidcast/csv_importer.py

@@ -16,7 +16,7 @@
 from delphi_utils import Nans
 from delphi.utils.epiweek import delta_epiweeks
 from delphi.epidata.common.covidcast_row import CovidcastRow
-from delphi.epidata.common.logger import get_structured_logger
+from delphi_logger import get_structured_logger
 
 DataFrameRow = NamedTuple('DFRow', [
   ('geo_id', str),

src/acquisition/covidcast/csv_to_database.py

@@ -11,7 +11,7 @@
 from delphi.epidata.acquisition.covidcast.csv_importer import CsvImporter, PathDetails
 from delphi.epidata.acquisition.covidcast.database import Database, DBLoadStateException
 from delphi.epidata.acquisition.covidcast.file_archiver import FileArchiver
-from delphi.epidata.common.logger import get_structured_logger
+from delphi_logger import get_structured_logger
 
 
 def get_argument_parser():

src/acquisition/covidcast/database.py

@@ -14,7 +14,7 @@
 
 # first party
 import delphi.operations.secrets as secrets
-from delphi.epidata.common.logger import get_structured_logger
+from delphi_logger import get_structured_logger
 from delphi.epidata.common.covidcast_row import CovidcastRow
 
 
@@ -117,28 +117,28 @@ def insert_or_update_batch(self, cc_rows: List[CovidcastRow], batch_size=2**20,
       get_structured_logger("insert_or_update_batch").fatal(err_msg)
       raise DBLoadStateException(err_msg)
 
-    # NOTE: `value_update_timestamp` is hardcoded to "NOW" (which is appropriate) and 
+    # NOTE: `value_update_timestamp` is hardcoded to "NOW" (which is appropriate) and
     #       `is_latest_issue` is hardcoded to 1 (which is temporary and addressed later in this method)
     insert_into_loader_sql = f'''
       INSERT INTO `{self.load_table}`
         (`source`, `signal`, `time_type`, `geo_type`, `time_value`, `geo_value`,
-        `value_updated_timestamp`, `value`, `stderr`, `sample_size`, `issue`, `lag`, 
+        `value_updated_timestamp`, `value`, `stderr`, `sample_size`, `issue`, `lag`,
         `is_latest_issue`, `missing_value`, `missing_stderr`, `missing_sample_size`)
       VALUES
-        (%s, %s, %s, %s, %s, %s, 
-        UNIX_TIMESTAMP(NOW()), %s, %s, %s, %s, %s, 
+        (%s, %s, %s, %s, %s, %s,
+        UNIX_TIMESTAMP(NOW()), %s, %s, %s, %s, %s,
         1, %s, %s, %s)
     '''
 
     # all load table entries are already marked "is_latest_issue".
     # if an entry in the load table is NOT in the latest table, it is clearly now the latest value for that key (so we do nothing (thanks to INNER join)).
     # if an entry *IS* in both load and latest tables, but latest table issue is newer, unmark is_latest_issue in load.
     fix_is_latest_issue_sql = f'''
-        UPDATE 
-            `{self.load_table}` JOIN `{self.latest_view}` 
-                USING (`source`, `signal`, `geo_type`, `geo_value`, `time_type`, `time_value`) 
-            SET `{self.load_table}`.`is_latest_issue`=0 
-            WHERE `{self.load_table}`.`issue` < `{self.latest_view}`.`issue` 
+        UPDATE
+            `{self.load_table}` JOIN `{self.latest_view}`
+                USING (`source`, `signal`, `geo_type`, `geo_value`, `time_type`, `time_value`)
+            SET `{self.load_table}`.`is_latest_issue`=0
+            WHERE `{self.load_table}`.`issue` < `{self.latest_view}`.`issue`
     '''
 
     # TODO: consider handling cc_rows as a generator instead of a list

src/acquisition/covidcast/file_archiver.py

@@ -6,7 +6,7 @@
 import shutil
 
 # first party
-from delphi.epidata.common.logger import get_structured_logger
+from delphi_logger import get_structured_logger
 
 class FileArchiver:
   """Archives files by moving and compressing."""

src/client/delphi_epidata.py

@@ -16,7 +16,7 @@
 
 from aiohttp import ClientSession, TCPConnector, BasicAuth
 
-from delphi_utils.logger import get_structured_logger
+from delphi_logger import get_structured_logger
 
 __version__ = "4.1.23"