From 9be4c9fb2e151ffd53a20aadb67146d7dd4d70a9 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Mon, 18 Jul 2022 19:17:02 -0400
Subject: [PATCH 01/20] store backfill file

---
 .../delphi_quidel_covidtest/pull.py           | 38 +++++++++++++++++++
 .../delphi_quidel_covidtest/run.py            |  7 +++-
 quidel_covidtest/params.json.template         |  1 +
 3 files changed, 45 insertions(+), 1 deletion(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py
index ab397ce47..f136e217b 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/pull.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py
@@ -8,8 +8,12 @@
 import pandas as pd
 import numpy as np
 
+from delphi_utils import GeoMapper
+
 from .constants import AGE_GROUPS
 
+gmpr = GeoMapper()
+
 def get_from_s3(start_date, end_date, bucket, logger):
     """
     Get raw data from aws s3 bucket.
@@ -57,6 +61,8 @@ def get_from_s3(start_date, end_date, bucket, logger):
 
             # Fetch data received on the same day
             for fn in s3_files[search_date]:
+                if ".csv" not in fn:
+                    continue  #Add to avoid that the folder name was readed as a fn.
                 if fn in set(df["fname"].values):
                     continue
                 obj = bucket.Object(key=fn)
@@ -370,3 +376,35 @@ def update_cache_file(df, _end_date, cache_dir):
         if ".csv" in fn:
             os.remove(join(cache_dir, fn))
     df.to_csv(join(cache_dir, "pulled_until_%s.csv") % _end_date.strftime("%Y%m%d"), index=False)
+
+def store_backfill_file(df, _end_date, backfill_dir):
+    """
+    Store county level backfill data into backfill_dir.
+
+    Parameter:
+        df: pd.DataFrame
+            Pre-process file at ZipCode level
+        _end_date:
+            The most recent date when the raw data is received
+        backfill_dir:
+            specified path to store backfill files.
+    """
+    backfilldata = df.copy()
+    backfilldata = gmpr.replace_geocode(backfilldata, from_code="zip", new_code="fips",
+                          from_col="zip", new_col="fips", date_col="timestamp")
+    backfilldata.rename({"timestamp": "time_value"}, axis=1, inplace=True)
+    _start_date = _end_date.replace(year=_end_date.year-1)
+    selected_columns = ['time_value', 'fips', 
+                        'totalTest_total', 'positiveTest_total', 
+                        'positiveTest_age_0_4', 'totalTest_age_0_4',
+                        'positiveTest_age_5_17', 'totalTest_age_5_17',
+                        'positiveTest_age_18_49', 'totalTest_age_18_49',
+                        'positiveTest_age_50_64', 'totalTest_age_50_64',
+                        'positiveTest_age_65plus', 'totalTest_age_65plus',
+                        'positiveTest_age_0_17', 'totalTest_age_0_17']
+    backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date, 
+                                    selected_columns]
+    path = backfill_dir + \
+        "/quidel_covidtest_as_of_%s"%datetime.strftime(_end_date, "%Y%m%d") + ".parquet"
+    # Store intermediate file into the backfill folder
+    backfilldata.to_parquet(path)    
diff --git a/quidel_covidtest/delphi_quidel_covidtest/run.py b/quidel_covidtest/delphi_quidel_covidtest/run.py
index fb1a69ac2..bf9289143 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/run.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/run.py
@@ -25,7 +25,8 @@
 from .pull import (pull_quidel_covidtest,
                    check_export_start_date,
                    check_export_end_date,
-                   update_cache_file)
+                   update_cache_file,
+                   store_backfill_file)
 
 
 def log_exit(start_time, stats, logger):
@@ -85,6 +86,7 @@ def run_module(params: Dict[str, Any]):
     stats = []
     atexit.register(log_exit, start_time, stats, logger)
     cache_dir = params["indicator"]["input_cache_dir"]
+    backfill_dir = params["indicator"]["backfill_dir"]
     export_dir = params["common"]["export_dir"]
     export_start_date = params["indicator"]["export_start_date"]
     export_end_date = params["indicator"]["export_end_date"]
@@ -95,6 +97,9 @@ def run_module(params: Dict[str, Any]):
     if _end_date is None:
         logger.info("The data is up-to-date. Currently, no new data to be ingested.")
         return
+    else:
+        # Store the backfill intermediate file
+        store_backfill_file(df, _end_date, backfill_dir)
     export_end_date = check_export_end_date(
         export_end_date, _end_date, END_FROM_TODAY_MINUS)
     export_start_date = check_export_start_date(
diff --git a/quidel_covidtest/params.json.template b/quidel_covidtest/params.json.template
index e96d2ccbc..ad1755252 100644
--- a/quidel_covidtest/params.json.template
+++ b/quidel_covidtest/params.json.template
@@ -7,6 +7,7 @@
   "indicator": {
     "static_file_dir": "./static",
     "input_cache_dir": "./cache",
+    "backfill_dir": "./backfill",
     "export_start_date": "2020-05-26",
     "export_end_date": "",
     "pull_start_date": "2020-05-26",

From c943a2ca250c08b885d26f3c583fb762bb0e11fb Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Mon, 18 Jul 2022 19:34:46 -0400
Subject: [PATCH 02/20] add pyarrow as a necessary package

---
 quidel_covidtest/setup.py          | 1 +
 quidel_covidtest/tests/test_run.py | 1 +
 2 files changed, 2 insertions(+)

diff --git a/quidel_covidtest/setup.py b/quidel_covidtest/setup.py
index 4c01e8593..369ac30c0 100644
--- a/quidel_covidtest/setup.py
+++ b/quidel_covidtest/setup.py
@@ -4,6 +4,7 @@
 required = [
     "numpy",
     "pandas",
+    "pyarrow",
     "pydocstyle",
     "pytest",
     "pytest-cov",
diff --git a/quidel_covidtest/tests/test_run.py b/quidel_covidtest/tests/test_run.py
index d9e28108a..16ff0e7bd 100644
--- a/quidel_covidtest/tests/test_run.py
+++ b/quidel_covidtest/tests/test_run.py
@@ -21,6 +21,7 @@ class TestRun:
         "indicator": {
             "static_file_dir": "../static",
             "input_cache_dir": "./cache",
+            "backfill_dir": "./backfill",
             "export_start_date": "2020-06-30",
             "export_end_date": "",
             "pull_start_date": "2020-07-09",

From 371f85d56e8a3b8da816e0d8e41047cc9be54cbd Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Mon, 18 Jul 2022 21:16:10 -0400
Subject: [PATCH 03/20] fix linting errors

---
 quidel_covidtest/delphi_quidel_covidtest/pull.py | 8 ++++----
 quidel_covidtest/delphi_quidel_covidtest/run.py  | 5 ++---
 2 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py
index f136e217b..91607c91b 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/pull.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py
@@ -394,17 +394,17 @@ def store_backfill_file(df, _end_date, backfill_dir):
                           from_col="zip", new_col="fips", date_col="timestamp")
     backfilldata.rename({"timestamp": "time_value"}, axis=1, inplace=True)
     _start_date = _end_date.replace(year=_end_date.year-1)
-    selected_columns = ['time_value', 'fips', 
-                        'totalTest_total', 'positiveTest_total', 
+    selected_columns = ['time_value', 'fips',
+                        'totalTest_total', 'positiveTest_total',
                         'positiveTest_age_0_4', 'totalTest_age_0_4',
                         'positiveTest_age_5_17', 'totalTest_age_5_17',
                         'positiveTest_age_18_49', 'totalTest_age_18_49',
                         'positiveTest_age_50_64', 'totalTest_age_50_64',
                         'positiveTest_age_65plus', 'totalTest_age_65plus',
                         'positiveTest_age_0_17', 'totalTest_age_0_17']
-    backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date, 
+    backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
                                     selected_columns]
     path = backfill_dir + \
         "/quidel_covidtest_as_of_%s"%datetime.strftime(_end_date, "%Y%m%d") + ".parquet"
     # Store intermediate file into the backfill folder
-    backfilldata.to_parquet(path)    
+    backfilldata.to_parquet(path)
diff --git a/quidel_covidtest/delphi_quidel_covidtest/run.py b/quidel_covidtest/delphi_quidel_covidtest/run.py
index bf9289143..db92a7722 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/run.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/run.py
@@ -97,9 +97,8 @@ def run_module(params: Dict[str, Any]):
     if _end_date is None:
         logger.info("The data is up-to-date. Currently, no new data to be ingested.")
         return
-    else:
-        # Store the backfill intermediate file
-        store_backfill_file(df, _end_date, backfill_dir)
+    # Store the backfill intermediate file
+    store_backfill_file(df, _end_date, backfill_dir)
     export_end_date = check_export_end_date(
         export_end_date, _end_date, END_FROM_TODAY_MINUS)
     export_start_date = check_export_start_date(

From 36c714cb85542b3cd8537b7cd8c4cfd3b4bb2eaa Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Mon, 18 Jul 2022 21:27:44 -0400
Subject: [PATCH 04/20] add the backfill folder for the unit test

---
 quidel_covidtest/tests/backfill/.gitignore | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 quidel_covidtest/tests/backfill/.gitignore

diff --git a/quidel_covidtest/tests/backfill/.gitignore b/quidel_covidtest/tests/backfill/.gitignore
new file mode 100644
index 000000000..afed0735d
--- /dev/null
+++ b/quidel_covidtest/tests/backfill/.gitignore
@@ -0,0 +1 @@
+*.csv

From 67bf5103325614c73bef6bc692772a22b9ffa24c Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Mon, 18 Jul 2022 21:49:33 -0400
Subject: [PATCH 05/20] update the comment for the params argument

---
 quidel_covidtest/delphi_quidel_covidtest/run.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/run.py b/quidel_covidtest/delphi_quidel_covidtest/run.py
index db92a7722..411999d9c 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/run.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/run.py
@@ -67,6 +67,7 @@ def run_module(params: Dict[str, Any]):
     - indicator":
         - "static_file_dir": str, directory name with population information
         - "input_cache_dir": str, directory in which to cache input data
+        - "backfill_dir": str, directory in which to store the backfill files
         - "export_start_date": str, YYYY-MM-DD format of earliest date to create output
         - "export_end_date": str, YYYY-MM-DD format of latest date to create output or "" to create
                              through the present

From 0c4daaf15782eeeb0dadcd22c4c32643030597f3 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Wed, 3 Aug 2022 23:35:13 -0400
Subject: [PATCH 06/20] update code for backfill

---
 .../delphi_quidel_covidtest/pull.py           | 65 ++++++++++++++++++-
 .../delphi_quidel_covidtest/run.py            |  8 ++-
 quidel_covidtest/params.json.template         |  1 +
 3 files changed, 70 insertions(+), 4 deletions(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py
index 91607c91b..eed41316f 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/pull.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py
@@ -2,6 +2,7 @@
 """Collect and process Quidel export files."""
 from os.path import join
 import os
+import glob
 from datetime import datetime, timedelta
 import boto3
 
@@ -384,15 +385,16 @@ def store_backfill_file(df, _end_date, backfill_dir):
     Parameter:
         df: pd.DataFrame
             Pre-process file at ZipCode level
-        _end_date:
+        _end_date: datetime
             The most recent date when the raw data is received
-        backfill_dir:
+        backfill_dir: str
             specified path to store backfill files.
     """
     backfilldata = df.copy()
     backfilldata = gmpr.replace_geocode(backfilldata, from_code="zip", new_code="fips",
                           from_col="zip", new_col="fips", date_col="timestamp")
     backfilldata.rename({"timestamp": "time_value"}, axis=1, inplace=True)
+    #Store one year's backfill data
     _start_date = _end_date.replace(year=_end_date.year-1)
     selected_columns = ['time_value', 'fips',
                         'totalTest_total', 'positiveTest_total',
@@ -405,6 +407,63 @@ def store_backfill_file(df, _end_date, backfill_dir):
     backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
                                     selected_columns]
     path = backfill_dir + \
-        "/quidel_covidtest_as_of_%s"%datetime.strftime(_end_date, "%Y%m%d") + ".parquet"
+        "/quidel_covidtest_as_of_%s.parquet"%datetime.strftime(_end_date, "%Y%m%d")
     # Store intermediate file into the backfill folder
     backfilldata.to_parquet(path)
+
+def merge_backfill_file(backfill_dir, backfill_merge_day, today,
+                        test_mode=False, check_nd=25):
+    """
+    Merge ~4 weeks' backfill data into one file.
+
+    Usually this function should merge 28 days' data into a new file so as to
+    save the reading time when running the backfill pipelines. We
+
+    Parameters
+    ----------
+    _end_date : datetime
+        The most recent date when the raw data is received
+    backfill_dir : str
+        specified path to store backfill files.
+    backfill_merge_day: int
+        The day of a week that we used to merge the backfill files. e.g. 0
+        is Monday.
+    test_mode: bool
+    check_nd: int
+        The criteria of the number of unmerged files. Ideally, we want the
+        number to be 28, but we use a looser criteria from practical
+        considerations
+    """
+    new_files = glob.glob(backfill_dir + "/quidel_covidtest_as_of_*")
+
+    def get_date(file_link):
+        # Keep the function here consistent with the backfill path in
+        # function `store_backfill_file`
+        fn = file_link.split("/")[-1].split(".parquet")[0].split("_")[-1]
+        return datetime.strptime(fn, "%Y%m%d")
+
+    date_list = list(map(get_date, new_files))
+    earliest_date = min(date_list)
+    latest_date = max(date_list)
+
+    # Check whether to merge
+    # Check the number of files that are not merged
+    if today.weekday() != backfill_merge_day or (today-earliest_date).days <= check_nd:
+        return
+
+    # Start to merge files
+    pdList = []
+    for fn in new_files:
+        df = pd.read_parquet(fn, engine='pyarrow')
+        pdList.append(df)
+    merged_file = pd.concat(pdList).sort_values(["time_value", "fips"])
+    path = backfill_dir + "/quidel_covidtest_from_%s_to_%s.parquet"%(
+        datetime.strftime(earliest_date, "%Y%m%d"),
+        datetime.strftime(latest_date, "%Y%m%d"))
+    merged_file.to_parquet(path)
+
+    # Delete daily files once we have the merged one.
+    if not test_mode:
+        for fn in new_files:
+            os.remove(fn)
+    return
diff --git a/quidel_covidtest/delphi_quidel_covidtest/run.py b/quidel_covidtest/delphi_quidel_covidtest/run.py
index 411999d9c..c18a543ed 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/run.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/run.py
@@ -26,7 +26,8 @@
                    check_export_start_date,
                    check_export_end_date,
                    update_cache_file,
-                   store_backfill_file)
+                   store_backfill_file,
+                   merge_backfill_file)
 
 
 def log_exit(start_time, stats, logger):
@@ -88,6 +89,7 @@ def run_module(params: Dict[str, Any]):
     atexit.register(log_exit, start_time, stats, logger)
     cache_dir = params["indicator"]["input_cache_dir"]
     backfill_dir = params["indicator"]["backfill_dir"]
+    backfill_merge_day = params["indicator"]["backfill_merge_day"]
     export_dir = params["common"]["export_dir"]
     export_start_date = params["indicator"]["export_start_date"]
     export_end_date = params["indicator"]["export_end_date"]
@@ -95,6 +97,10 @@ def run_module(params: Dict[str, Any]):
 
     # Pull data and update export date
     df, _end_date = pull_quidel_covidtest(params["indicator"], logger)
+    # Merge 4 weeks' data into one file to save runtime
+    # Notice that here we don't check the _end_date(receive date)
+    # since we always want such merging happens on a certain day of a week
+    merge_backfill_file(backfill_dir, backfill_merge_day, datetime.today())
     if _end_date is None:
         logger.info("The data is up-to-date. Currently, no new data to be ingested.")
         return
diff --git a/quidel_covidtest/params.json.template b/quidel_covidtest/params.json.template
index ad1755252..d05ecd25e 100644
--- a/quidel_covidtest/params.json.template
+++ b/quidel_covidtest/params.json.template
@@ -8,6 +8,7 @@
     "static_file_dir": "./static",
     "input_cache_dir": "./cache",
     "backfill_dir": "./backfill",
+    "backfill_merge_day": 0,
     "export_start_date": "2020-05-26",
     "export_end_date": "",
     "pull_start_date": "2020-05-26",

From 7ab17e8969938755f4fa4164ff747e2f4db4cc49 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Wed, 3 Aug 2022 23:35:39 -0400
Subject: [PATCH 07/20] fx unit tests

---
 quidel_covidtest/tests/test_pull.py | 71 ++++++++++++++++++++++++++++-
 quidel_covidtest/tests/test_run.py  |  1 +
 2 files changed, 71 insertions(+), 1 deletion(-)

diff --git a/quidel_covidtest/tests/test_pull.py b/quidel_covidtest/tests/test_pull.py
index ae35fc68f..df1cbde7b 100644
--- a/quidel_covidtest/tests/test_pull.py
+++ b/quidel_covidtest/tests/test_pull.py
@@ -1,4 +1,6 @@
 import logging
+import os 
+import glob
 from datetime import datetime
 
 import pandas as pd
@@ -9,7 +11,9 @@
     pull_quidel_covidtest,
     check_intermediate_file,
     check_export_end_date,
-    check_export_start_date
+    check_export_start_date,
+    store_backfill_file,
+    merge_backfill_file
 )
 from delphi_quidel_covidtest.constants import AGE_GROUPS
 
@@ -17,6 +21,7 @@
 EXPORT_DAY_RANGE = 40
 
 TEST_LOGGER = logging.getLogger()
+backfill_dir="./backfill"
 
 class TestFixData:
     def test_fix_zipcode(self):
@@ -103,3 +108,67 @@ def test_check_export_start_date(self):
         expected = [datetime(2020, 5, 26), datetime(2020, 6, 20), datetime(2020, 5, 26)]
 
         assert tested == expected
+        
+    def store_backfill_file(self):
+        df, _end_date = pull_quidel_covidtest({
+            "static_file_dir": "../static",
+            "input_cache_dir": "./cache",
+            "export_start_date": "2020-06-30",
+            "export_end_date": "",
+            "pull_start_date": "2020-07-09",
+            "pull_end_date":"",
+            "aws_credentials": {
+                "aws_access_key_id": "",
+                "aws_secret_access_key": ""
+            },
+            "bucket_name": "",
+            "wip_signal": "",
+            "test_mode": True
+        }, TEST_LOGGER)
+        
+        store_backfill_file(df, _end_date, backfill_dir)
+        fn = "quidel_covidtest_as_of_20200817.parquet"
+        backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')
+        
+        selected_columns = ['time_value', 'fips',
+                        'totalTest_total', 'positiveTest_total',
+                        'positiveTest_age_0_4', 'totalTest_age_0_4',
+                        'positiveTest_age_5_17', 'totalTest_age_5_17',
+                        'positiveTest_age_18_49', 'totalTest_age_18_49',
+                        'positiveTest_age_50_64', 'totalTest_age_50_64',
+                        'positiveTest_age_65plus', 'totalTest_age_65plus',
+                        'positiveTest_age_0_17', 'totalTest_age_0_17']
+        assert set(selected_columns) == set(backfill_df.columns)       
+        
+    def test_merge_backfill_file(self):
+        
+        today = datetime.today()
+        new_files = glob.glob(backfill_dir + "/*.parquet")
+        fn = "quidel_covidtest_from_20200817_to_20200820.parquet"
+        assert fn not in os.listdir(backfill_dir)
+        
+        # Check the when the merged file is not generated
+        today = datetime(2020, 8, 20)
+        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=8)
+        assert fn not in os.listdir(backfill_dir)
+        
+         # Generate the merged file, but not delete it
+        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=2)         
+        assert fn in os.listdir(backfill_dir)
+
+        # Read daily file
+        pdList = []        
+        for file in new_files:
+            df = pd.read_parquet(file, engine='pyarrow')
+            pdList.append(df)
+        expected = pd.concat(pdList).sort_values(["time_value", "fips"])
+        
+        # Read the merged file
+        merged = pd.read_parquet(backfill_dir + "/" + fn, engine='pyarrow')
+        
+        assert expected.shape[0] == merged.shape[0]
+        assert expected.shape[1] == merged.shape[1]
+        
+        os.remove(backfill_dir + "/" + fn)
+        assert fn not in os.listdir(backfill_dir)
+        
diff --git a/quidel_covidtest/tests/test_run.py b/quidel_covidtest/tests/test_run.py
index 16ff0e7bd..4e15bea91 100644
--- a/quidel_covidtest/tests/test_run.py
+++ b/quidel_covidtest/tests/test_run.py
@@ -22,6 +22,7 @@ class TestRun:
             "static_file_dir": "../static",
             "input_cache_dir": "./cache",
             "backfill_dir": "./backfill",
+            "backfill_merge_day": 0,
             "export_start_date": "2020-06-30",
             "export_end_date": "",
             "pull_start_date": "2020-07-09",

From f3049d324680eaced2f1498929f75b5e794315d4 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Wed, 3 Aug 2022 23:39:47 -0400
Subject: [PATCH 08/20] add backfill files for unit tests

---
 .../quidel_covidtest_as_of_20200817.parquet     | Bin 0 -> 14543 bytes
 .../quidel_covidtest_as_of_20200818.parquet     | Bin 0 -> 14543 bytes
 .../quidel_covidtest_as_of_20200819.parquet     | Bin 0 -> 14543 bytes
 .../quidel_covidtest_as_of_20200820.parquet     | Bin 0 -> 14543 bytes
 4 files changed, 0 insertions(+), 0 deletions(-)
 create mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet
 create mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200818.parquet
 create mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200819.parquet
 create mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200820.parquet

diff --git a/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet b/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet
new file mode 100644
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From 199a47356953fade890c12f38e755885d7336408 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Thu, 4 Aug 2022 01:41:22 -0400
Subject: [PATCH 09/20] update column names'

---
 .../delphi_quidel_covidtest/pull.py           |  33 +++++++++++++-----
 .../quidel_covidtest_as_of_20200817.parquet   | Bin 14543 -> 13610 bytes
 .../quidel_covidtest_as_of_20200818.parquet   | Bin 14543 -> 13603 bytes
 .../quidel_covidtest_as_of_20200819.parquet   | Bin 14543 -> 13603 bytes
 .../quidel_covidtest_as_of_20200820.parquet   | Bin 14543 -> 13603 bytes
 quidel_covidtest/tests/test_pull.py           |  25 +++++++------
 6 files changed, 39 insertions(+), 19 deletions(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py
index eed41316f..da516cd49 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/pull.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py
@@ -393,17 +393,32 @@ def store_backfill_file(df, _end_date, backfill_dir):
     backfilldata = df.copy()
     backfilldata = gmpr.replace_geocode(backfilldata, from_code="zip", new_code="fips",
                           from_col="zip", new_col="fips", date_col="timestamp")
-    backfilldata.rename({"timestamp": "time_value"}, axis=1, inplace=True)
+    backfilldata.rename({"timestamp": "time_value",
+                         "totalTest_total": "den_total",
+                         "positiveTest_total": "num_total",
+                        "positiveTest_age_0_4": "num_age_0_4",
+                        "totalTest_age_0_4": "den_age_0_4",
+                        "positiveTest_age_5_17": "num_age_5_17",
+                        "totalTest_age_5_17": "den_age_5_17",
+                        "positiveTest_age_18_49": "num_age_18_49",
+                        "totalTest_age_18_49": "den_age_18_49",
+                        "positiveTest_age_50_64": "num_age_50_64",
+                        "totalTest_age_50_64": "den_age_50_64",
+                        "positiveTest_age_65plus": "num_age_65plus",
+                        "totalTest_age_65plus": "den_age_65plus",
+                        "positiveTest_age_0_17": "num_age_0_17",
+                        "totalTest_age_0_17": "den_age_0_17"},
+                        axis=1, inplace=True)
     #Store one year's backfill data
     _start_date = _end_date.replace(year=_end_date.year-1)
     selected_columns = ['time_value', 'fips',
-                        'totalTest_total', 'positiveTest_total',
-                        'positiveTest_age_0_4', 'totalTest_age_0_4',
-                        'positiveTest_age_5_17', 'totalTest_age_5_17',
-                        'positiveTest_age_18_49', 'totalTest_age_18_49',
-                        'positiveTest_age_50_64', 'totalTest_age_50_64',
-                        'positiveTest_age_65plus', 'totalTest_age_65plus',
-                        'positiveTest_age_0_17', 'totalTest_age_0_17']
+                        'den_total', 'num_total',
+                        'num_age_0_4', 'den_age_0_4',
+                        'num_age_5_17', 'den_age_5_17',
+                        'num_age_18_49', 'den_age_18_49',
+                        'num_age_50_64', 'den_age_50_64',
+                        'num_age_65plus', 'den_age_65plus',
+                        'num_age_0_17', 'den_age_0_17']
     backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
                                     selected_columns]
     path = backfill_dir + \
@@ -421,7 +436,7 @@ def merge_backfill_file(backfill_dir, backfill_merge_day, today,
 
     Parameters
     ----------
-    _end_date : datetime
+    today : datetime
         The most recent date when the raw data is received
     backfill_dir : str
         specified path to store backfill files.
diff --git a/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet b/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet
index 008b7f74cc8d4c86bcf991cc29a4968a08ff98fd..0e730fd5a928c983f46722abc431f27e34e95e08 100644
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diff --git a/quidel_covidtest/tests/test_pull.py b/quidel_covidtest/tests/test_pull.py
index df1cbde7b..27ba1a55d 100644
--- a/quidel_covidtest/tests/test_pull.py
+++ b/quidel_covidtest/tests/test_pull.py
@@ -126,19 +126,24 @@ def store_backfill_file(self):
             "test_mode": True
         }, TEST_LOGGER)
         
-        store_backfill_file(df, _end_date, backfill_dir)
-        fn = "quidel_covidtest_as_of_20200817.parquet"
+        store_backfill_file(df, datetime(2020, 1, 1), backfill_dir)
+        fn = "quidel_covidtest_as_of_20200101.parquet"
+        assert fn in os.listdir(backfill_dir)
+        
         backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')
         
         selected_columns = ['time_value', 'fips',
-                        'totalTest_total', 'positiveTest_total',
-                        'positiveTest_age_0_4', 'totalTest_age_0_4',
-                        'positiveTest_age_5_17', 'totalTest_age_5_17',
-                        'positiveTest_age_18_49', 'totalTest_age_18_49',
-                        'positiveTest_age_50_64', 'totalTest_age_50_64',
-                        'positiveTest_age_65plus', 'totalTest_age_65plus',
-                        'positiveTest_age_0_17', 'totalTest_age_0_17']
-        assert set(selected_columns) == set(backfill_df.columns)       
+                        'den_total', 'num_total',
+                        'num_age_0_4', 'den_age_0_4',
+                        'num_age_5_17', 'den_age_5_17',
+                        'num_age_18_49', 'den_age_18_49',
+                        'num_age_50_64', 'den_age_50_64',
+                        'num_age_65plus', 'den_age_65plus',
+                        'num_age_0_17', 'den_age_0_17']
+        assert set(selected_columns) == set(backfill_df.columns)  
+        
+        os.remove(backfill_dir + "/" + fn)
+        assert fn not in os.listdir(backfill_dir)
         
     def test_merge_backfill_file(self):
         

From 190e21b6102a6c74efdce20e6f339d4920011526 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Thu, 4 Aug 2022 16:58:02 -0400
Subject: [PATCH 10/20] move all the backfill related functions to another
 script

---
 .../delphi_quidel_covidtest/backfill.py       | 117 ++++++++++++++++++
 .../delphi_quidel_covidtest/pull.py           | 106 ----------------
 .../delphi_quidel_covidtest/run.py            |   6 +-
 quidel_covidtest/tests/test_backfill.py       |  88 +++++++++++++
 quidel_covidtest/tests/test_pull.py           |  73 +----------
 5 files changed, 208 insertions(+), 182 deletions(-)
 create mode 100644 quidel_covidtest/delphi_quidel_covidtest/backfill.py
 create mode 100644 quidel_covidtest/tests/test_backfill.py

diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
new file mode 100644
index 000000000..7ca723130
--- /dev/null
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -0,0 +1,117 @@
+# -*- coding: utf-8 -*-
+"""Store backfill data."""
+import os
+import glob
+from datetime import datetime
+
+import pandas as pd
+
+from delphi_utils import GeoMapper
+
+
+gmpr = GeoMapper()
+
+def store_backfill_file(df, _end_date, backfill_dir):
+    """
+    Store county level backfill data into backfill_dir.
+
+    Parameter:
+        df: pd.DataFrame
+            Pre-process file at ZipCode level
+        _end_date: datetime
+            The most recent date when the raw data is received
+        backfill_dir: str
+            specified path to store backfill files.
+    """
+    backfilldata = df.copy()
+    backfilldata = gmpr.replace_geocode(backfilldata, from_code="zip", new_code="fips",
+                          from_col="zip", new_col="fips", date_col="timestamp")
+    backfilldata.rename({"timestamp": "time_value",
+                         "totalTest_total": "den_total",
+                         "positiveTest_total": "num_total",
+                        "positiveTest_age_0_4": "num_age_0_4",
+                        "totalTest_age_0_4": "den_age_0_4",
+                        "positiveTest_age_5_17": "num_age_5_17",
+                        "totalTest_age_5_17": "den_age_5_17",
+                        "positiveTest_age_18_49": "num_age_18_49",
+                        "totalTest_age_18_49": "den_age_18_49",
+                        "positiveTest_age_50_64": "num_age_50_64",
+                        "totalTest_age_50_64": "den_age_50_64",
+                        "positiveTest_age_65plus": "num_age_65plus",
+                        "totalTest_age_65plus": "den_age_65plus",
+                        "positiveTest_age_0_17": "num_age_0_17",
+                        "totalTest_age_0_17": "den_age_0_17"},
+                        axis=1, inplace=True)
+    #Store one year's backfill data
+    _start_date = _end_date.replace(year=_end_date.year-1)
+    selected_columns = ['time_value', 'fips',
+                        'den_total', 'num_total',
+                        'num_age_0_4', 'den_age_0_4',
+                        'num_age_5_17', 'den_age_5_17',
+                        'num_age_18_49', 'den_age_18_49',
+                        'num_age_50_64', 'den_age_50_64',
+                        'num_age_65plus', 'den_age_65plus',
+                        'num_age_0_17', 'den_age_0_17']
+    backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
+                                    selected_columns]
+    path = backfill_dir + \
+        "/quidel_covidtest_as_of_%s.parquet"%datetime.strftime(_end_date, "%Y%m%d")
+    # Store intermediate file into the backfill folder
+    backfilldata.to_parquet(path)
+
+def merge_backfill_file(backfill_dir, backfill_merge_day, today,
+                        test_mode=False, check_nd=25):
+    """
+    Merge ~4 weeks' backfill data into one file.
+
+    Usually this function should merge 28 days' data into a new file so as to
+    save the reading time when running the backfill pipelines. We
+
+    Parameters
+    ----------
+    today : datetime
+        The most recent date when the raw data is received
+    backfill_dir : str
+        specified path to store backfill files.
+    backfill_merge_day: int
+        The day of a week that we used to merge the backfill files. e.g. 0
+        is Monday.
+    test_mode: bool
+    check_nd: int
+        The criteria of the number of unmerged files. Ideally, we want the
+        number to be 28, but we use a looser criteria from practical
+        considerations
+    """
+    new_files = glob.glob(backfill_dir + "/quidel_covidtest_as_of_*")
+
+    def get_date(file_link):
+        # Keep the function here consistent with the backfill path in
+        # function `store_backfill_file`
+        fn = file_link.split("/")[-1].split(".parquet")[0].split("_")[-1]
+        return datetime.strptime(fn, "%Y%m%d")
+
+    date_list = list(map(get_date, new_files))
+    earliest_date = min(date_list)
+    latest_date = max(date_list)
+
+    # Check whether to merge
+    # Check the number of files that are not merged
+    if today.weekday() != backfill_merge_day or (today-earliest_date).days <= check_nd:
+        return
+
+    # Start to merge files
+    pdList = []
+    for fn in new_files:
+        df = pd.read_parquet(fn, engine='pyarrow')
+        pdList.append(df)
+    merged_file = pd.concat(pdList).sort_values(["time_value", "fips"])
+    path = backfill_dir + "/quidel_covidtest_from_%s_to_%s.parquet"%(
+        datetime.strftime(earliest_date, "%Y%m%d"),
+        datetime.strftime(latest_date, "%Y%m%d"))
+    merged_file.to_parquet(path)
+
+    # Delete daily files once we have the merged one.
+    if not test_mode:
+        for fn in new_files:
+            os.remove(fn)
+    return
diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py
index da516cd49..c2357b64b 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/pull.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py
@@ -2,7 +2,6 @@
 """Collect and process Quidel export files."""
 from os.path import join
 import os
-import glob
 from datetime import datetime, timedelta
 import boto3
 
@@ -377,108 +376,3 @@ def update_cache_file(df, _end_date, cache_dir):
         if ".csv" in fn:
             os.remove(join(cache_dir, fn))
     df.to_csv(join(cache_dir, "pulled_until_%s.csv") % _end_date.strftime("%Y%m%d"), index=False)
-
-def store_backfill_file(df, _end_date, backfill_dir):
-    """
-    Store county level backfill data into backfill_dir.
-
-    Parameter:
-        df: pd.DataFrame
-            Pre-process file at ZipCode level
-        _end_date: datetime
-            The most recent date when the raw data is received
-        backfill_dir: str
-            specified path to store backfill files.
-    """
-    backfilldata = df.copy()
-    backfilldata = gmpr.replace_geocode(backfilldata, from_code="zip", new_code="fips",
-                          from_col="zip", new_col="fips", date_col="timestamp")
-    backfilldata.rename({"timestamp": "time_value",
-                         "totalTest_total": "den_total",
-                         "positiveTest_total": "num_total",
-                        "positiveTest_age_0_4": "num_age_0_4",
-                        "totalTest_age_0_4": "den_age_0_4",
-                        "positiveTest_age_5_17": "num_age_5_17",
-                        "totalTest_age_5_17": "den_age_5_17",
-                        "positiveTest_age_18_49": "num_age_18_49",
-                        "totalTest_age_18_49": "den_age_18_49",
-                        "positiveTest_age_50_64": "num_age_50_64",
-                        "totalTest_age_50_64": "den_age_50_64",
-                        "positiveTest_age_65plus": "num_age_65plus",
-                        "totalTest_age_65plus": "den_age_65plus",
-                        "positiveTest_age_0_17": "num_age_0_17",
-                        "totalTest_age_0_17": "den_age_0_17"},
-                        axis=1, inplace=True)
-    #Store one year's backfill data
-    _start_date = _end_date.replace(year=_end_date.year-1)
-    selected_columns = ['time_value', 'fips',
-                        'den_total', 'num_total',
-                        'num_age_0_4', 'den_age_0_4',
-                        'num_age_5_17', 'den_age_5_17',
-                        'num_age_18_49', 'den_age_18_49',
-                        'num_age_50_64', 'den_age_50_64',
-                        'num_age_65plus', 'den_age_65plus',
-                        'num_age_0_17', 'den_age_0_17']
-    backfilldata = backfilldata.loc[backfilldata["time_value"] >= _start_date,
-                                    selected_columns]
-    path = backfill_dir + \
-        "/quidel_covidtest_as_of_%s.parquet"%datetime.strftime(_end_date, "%Y%m%d")
-    # Store intermediate file into the backfill folder
-    backfilldata.to_parquet(path)
-
-def merge_backfill_file(backfill_dir, backfill_merge_day, today,
-                        test_mode=False, check_nd=25):
-    """
-    Merge ~4 weeks' backfill data into one file.
-
-    Usually this function should merge 28 days' data into a new file so as to
-    save the reading time when running the backfill pipelines. We
-
-    Parameters
-    ----------
-    today : datetime
-        The most recent date when the raw data is received
-    backfill_dir : str
-        specified path to store backfill files.
-    backfill_merge_day: int
-        The day of a week that we used to merge the backfill files. e.g. 0
-        is Monday.
-    test_mode: bool
-    check_nd: int
-        The criteria of the number of unmerged files. Ideally, we want the
-        number to be 28, but we use a looser criteria from practical
-        considerations
-    """
-    new_files = glob.glob(backfill_dir + "/quidel_covidtest_as_of_*")
-
-    def get_date(file_link):
-        # Keep the function here consistent with the backfill path in
-        # function `store_backfill_file`
-        fn = file_link.split("/")[-1].split(".parquet")[0].split("_")[-1]
-        return datetime.strptime(fn, "%Y%m%d")
-
-    date_list = list(map(get_date, new_files))
-    earliest_date = min(date_list)
-    latest_date = max(date_list)
-
-    # Check whether to merge
-    # Check the number of files that are not merged
-    if today.weekday() != backfill_merge_day or (today-earliest_date).days <= check_nd:
-        return
-
-    # Start to merge files
-    pdList = []
-    for fn in new_files:
-        df = pd.read_parquet(fn, engine='pyarrow')
-        pdList.append(df)
-    merged_file = pd.concat(pdList).sort_values(["time_value", "fips"])
-    path = backfill_dir + "/quidel_covidtest_from_%s_to_%s.parquet"%(
-        datetime.strftime(earliest_date, "%Y%m%d"),
-        datetime.strftime(latest_date, "%Y%m%d"))
-    merged_file.to_parquet(path)
-
-    # Delete daily files once we have the merged one.
-    if not test_mode:
-        for fn in new_files:
-            os.remove(fn)
-    return
diff --git a/quidel_covidtest/delphi_quidel_covidtest/run.py b/quidel_covidtest/delphi_quidel_covidtest/run.py
index c18a543ed..4f7f7fc8e 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/run.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/run.py
@@ -25,10 +25,8 @@
 from .pull import (pull_quidel_covidtest,
                    check_export_start_date,
                    check_export_end_date,
-                   update_cache_file,
-                   store_backfill_file,
-                   merge_backfill_file)
-
+                   update_cache_file)
+from .backfill import (store_backfill_file, merge_backfill_file)
 
 def log_exit(start_time, stats, logger):
     """Log at program exit."""
diff --git a/quidel_covidtest/tests/test_backfill.py b/quidel_covidtest/tests/test_backfill.py
new file mode 100644
index 000000000..b4a89ebe8
--- /dev/null
+++ b/quidel_covidtest/tests/test_backfill.py
@@ -0,0 +1,88 @@
+import logging
+import os 
+import glob
+from datetime import datetime
+
+import pandas as pd
+
+from delphi_quidel_covidtest.pull import pull_quidel_covidtest
+
+from delphi_quidel_covidtest.backfill import (store_backfill_file,
+                                              merge_backfill_file)
+
+END_FROM_TODAY_MINUS = 5
+EXPORT_DAY_RANGE = 40
+
+TEST_LOGGER = logging.getLogger()
+backfill_dir="./backfill"
+
+class TestBackfill:
+        
+    def test_store_backfill_file(self):
+        df, _end_date = pull_quidel_covidtest({
+            "static_file_dir": "../static",
+            "input_cache_dir": "./cache",
+            "export_start_date": "2020-06-30",
+            "export_end_date": "",
+            "pull_start_date": "2020-07-09",
+            "pull_end_date":"",
+            "aws_credentials": {
+                "aws_access_key_id": "",
+                "aws_secret_access_key": ""
+            },
+            "bucket_name": "",
+            "wip_signal": "",
+            "test_mode": True
+        }, TEST_LOGGER)
+        
+        store_backfill_file(df, datetime(2020, 1, 1), backfill_dir)
+        fn = "quidel_covidtest_as_of_20200101.parquet"
+        assert fn in os.listdir(backfill_dir)
+        
+        backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')
+        
+        selected_columns = ['time_value', 'fips',
+                        'den_total', 'num_total',
+                        'num_age_0_4', 'den_age_0_4',
+                        'num_age_5_17', 'den_age_5_17',
+                        'num_age_18_49', 'den_age_18_49',
+                        'num_age_50_64', 'den_age_50_64',
+                        'num_age_65plus', 'den_age_65plus',
+                        'num_age_0_17', 'den_age_0_17']
+        assert set(selected_columns) == set(backfill_df.columns)  
+        
+        os.remove(backfill_dir + "/" + fn)
+        assert fn not in os.listdir(backfill_dir)
+        
+    def test_merge_backfill_file(self):
+        
+        today = datetime.today()
+        new_files = glob.glob(backfill_dir + "/*.parquet")
+        fn = "quidel_covidtest_from_20200817_to_20200820.parquet"
+        assert fn not in os.listdir(backfill_dir)
+        
+        # Check the when the merged file is not generated
+        today = datetime(2020, 8, 20)
+        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=8)
+        assert fn not in os.listdir(backfill_dir)
+        
+         # Generate the merged file, but not delete it
+        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=2)         
+        assert fn in os.listdir(backfill_dir)
+
+        # Read daily file
+        pdList = []        
+        for file in new_files:
+            df = pd.read_parquet(file, engine='pyarrow')
+            pdList.append(df)
+        expected = pd.concat(pdList).sort_values(["time_value", "fips"])
+        
+        # Read the merged file
+        merged = pd.read_parquet(backfill_dir + "/" + fn, engine='pyarrow')
+        
+        assert expected.shape[0] == merged.shape[0]
+        assert expected.shape[1] == merged.shape[1]
+        
+        os.remove(backfill_dir + "/" + fn)
+        assert fn not in os.listdir(backfill_dir)
+        
diff --git a/quidel_covidtest/tests/test_pull.py b/quidel_covidtest/tests/test_pull.py
index 27ba1a55d..578401abf 100644
--- a/quidel_covidtest/tests/test_pull.py
+++ b/quidel_covidtest/tests/test_pull.py
@@ -11,9 +11,7 @@
     pull_quidel_covidtest,
     check_intermediate_file,
     check_export_end_date,
-    check_export_start_date,
-    store_backfill_file,
-    merge_backfill_file
+    check_export_start_date
 )
 from delphi_quidel_covidtest.constants import AGE_GROUPS
 
@@ -21,7 +19,6 @@
 EXPORT_DAY_RANGE = 40
 
 TEST_LOGGER = logging.getLogger()
-backfill_dir="./backfill"
 
 class TestFixData:
     def test_fix_zipcode(self):
@@ -109,71 +106,3 @@ def test_check_export_start_date(self):
 
         assert tested == expected
         
-    def store_backfill_file(self):
-        df, _end_date = pull_quidel_covidtest({
-            "static_file_dir": "../static",
-            "input_cache_dir": "./cache",
-            "export_start_date": "2020-06-30",
-            "export_end_date": "",
-            "pull_start_date": "2020-07-09",
-            "pull_end_date":"",
-            "aws_credentials": {
-                "aws_access_key_id": "",
-                "aws_secret_access_key": ""
-            },
-            "bucket_name": "",
-            "wip_signal": "",
-            "test_mode": True
-        }, TEST_LOGGER)
-        
-        store_backfill_file(df, datetime(2020, 1, 1), backfill_dir)
-        fn = "quidel_covidtest_as_of_20200101.parquet"
-        assert fn in os.listdir(backfill_dir)
-        
-        backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')
-        
-        selected_columns = ['time_value', 'fips',
-                        'den_total', 'num_total',
-                        'num_age_0_4', 'den_age_0_4',
-                        'num_age_5_17', 'den_age_5_17',
-                        'num_age_18_49', 'den_age_18_49',
-                        'num_age_50_64', 'den_age_50_64',
-                        'num_age_65plus', 'den_age_65plus',
-                        'num_age_0_17', 'den_age_0_17']
-        assert set(selected_columns) == set(backfill_df.columns)  
-        
-        os.remove(backfill_dir + "/" + fn)
-        assert fn not in os.listdir(backfill_dir)
-        
-    def test_merge_backfill_file(self):
-        
-        today = datetime.today()
-        new_files = glob.glob(backfill_dir + "/*.parquet")
-        fn = "quidel_covidtest_from_20200817_to_20200820.parquet"
-        assert fn not in os.listdir(backfill_dir)
-        
-        # Check the when the merged file is not generated
-        today = datetime(2020, 8, 20)
-        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=8)
-        assert fn not in os.listdir(backfill_dir)
-        
-         # Generate the merged file, but not delete it
-        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=2)         
-        assert fn in os.listdir(backfill_dir)
-
-        # Read daily file
-        pdList = []        
-        for file in new_files:
-            df = pd.read_parquet(file, engine='pyarrow')
-            pdList.append(df)
-        expected = pd.concat(pdList).sort_values(["time_value", "fips"])
-        
-        # Read the merged file
-        merged = pd.read_parquet(backfill_dir + "/" + fn, engine='pyarrow')
-        
-        assert expected.shape[0] == merged.shape[0]
-        assert expected.shape[1] == merged.shape[1]
-        
-        os.remove(backfill_dir + "/" + fn)
-        assert fn not in os.listdir(backfill_dir)
-        

From bdd2a87a1667df6b7d03289be2c385b26ff2ea12 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Thu, 4 Aug 2022 16:58:40 -0400
Subject: [PATCH 11/20] remove unused import

---
 quidel_covidtest/tests/test_pull.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/quidel_covidtest/tests/test_pull.py b/quidel_covidtest/tests/test_pull.py
index 578401abf..a3436392b 100644
--- a/quidel_covidtest/tests/test_pull.py
+++ b/quidel_covidtest/tests/test_pull.py
@@ -1,6 +1,4 @@
 import logging
-import os 
-import glob
 from datetime import datetime
 
 import pandas as pd

From a9cb4915a773c18b69f88646e5dc3f07213b8ec7 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Fri, 12 Aug 2022 14:28:03 -0400
Subject: [PATCH 12/20] add issue_date and lag to backfill file

---
 quidel_covidtest/delphi_quidel_covidtest/backfill.py | 3 +++
 quidel_covidtest/tests/test_backfill.py              | 4 ++++
 2 files changed, 7 insertions(+)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
index 7ca723130..9aed3e83f 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/backfill.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -103,6 +103,9 @@ def get_date(file_link):
     pdList = []
     for fn in new_files:
         df = pd.read_parquet(fn, engine='pyarrow')
+        issue_date = datetime.strptime(fn[-16:-8], "%Y%m%d")
+        df["issue_date"] = issue_date
+        df["lag"] = [(issue_date - x).days for x in df["time_value"]]
         pdList.append(df)
     merged_file = pd.concat(pdList).sort_values(["time_value", "fips"])
     path = backfill_dir + "/quidel_covidtest_from_%s_to_%s.parquet"%(
diff --git a/quidel_covidtest/tests/test_backfill.py b/quidel_covidtest/tests/test_backfill.py
index b4a89ebe8..35d82bf12 100644
--- a/quidel_covidtest/tests/test_backfill.py
+++ b/quidel_covidtest/tests/test_backfill.py
@@ -74,12 +74,16 @@ def test_merge_backfill_file(self):
         pdList = []        
         for file in new_files:
             df = pd.read_parquet(file, engine='pyarrow')
+            issue_date = datetime.strptime(file[-16:-8], "%Y%m%d")
+            df["issue_date"] = issue_date
+            df["lag"] = [(issue_date - x).days for x in df["time_value"]]
             pdList.append(df)
         expected = pd.concat(pdList).sort_values(["time_value", "fips"])
         
         # Read the merged file
         merged = pd.read_parquet(backfill_dir + "/" + fn, engine='pyarrow')
         
+        assert set(expected.columns) == set(merged.columns)
         assert expected.shape[0] == merged.shape[0]
         assert expected.shape[1] == merged.shape[1]
         

From 331a13817b2180b444bed28d908861888ce58504 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <31444565+jingjtang@users.noreply.github.com>
Date: Fri, 19 Aug 2022 21:04:22 -0400
Subject: [PATCH 13/20] Update ansible file for quidel_covidtest

---
 ansible/templates/quidel_covidtest-params-prod.json.j2 | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ansible/templates/quidel_covidtest-params-prod.json.j2 b/ansible/templates/quidel_covidtest-params-prod.json.j2
index fe605206b..c8f7ebf49 100644
--- a/ansible/templates/quidel_covidtest-params-prod.json.j2
+++ b/ansible/templates/quidel_covidtest-params-prod.json.j2
@@ -10,6 +10,8 @@
     "export_end_date": "",
     "pull_start_date": "2020-05-26",
     "pull_end_date":"",
+    "backfill_dir": "/common/backfill/quidel_covidtest",
+    "backfill_merge_day": 0,
     "export_day_range":40,
     "aws_credentials": {
       "aws_access_key_id": "{{ quidel_aws_access_key_id }}",

From 7a71cce3951d98fb36745e3ea35fa8a8d6951d07 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <31444565+jingjtang@users.noreply.github.com>
Date: Fri, 19 Aug 2022 21:10:55 -0400
Subject: [PATCH 14/20] Use get_date() for issue_date

---
 quidel_covidtest/delphi_quidel_covidtest/backfill.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
index 9aed3e83f..fa2b92ecb 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/backfill.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -103,7 +103,7 @@ def get_date(file_link):
     pdList = []
     for fn in new_files:
         df = pd.read_parquet(fn, engine='pyarrow')
-        issue_date = datetime.strptime(fn[-16:-8], "%Y%m%d")
+        issue_date = get_date(fn)
         df["issue_date"] = issue_date
         df["lag"] = [(issue_date - x).days for x in df["time_value"]]
         pdList.append(df)

From 008daa4bb42289461056cc59d39a5a107fffa66c Mon Sep 17 00:00:00 2001
From: Jingjing Tang <31444565+jingjtang@users.noreply.github.com>
Date: Fri, 19 Aug 2022 21:21:39 -0400
Subject: [PATCH 15/20] Finish the comment for merging

---
 quidel_covidtest/delphi_quidel_covidtest/backfill.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
index fa2b92ecb..65963612e 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/backfill.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -65,7 +65,8 @@ def merge_backfill_file(backfill_dir, backfill_merge_day, today,
     Merge ~4 weeks' backfill data into one file.
 
     Usually this function should merge 28 days' data into a new file so as to
-    save the reading time when running the backfill pipelines. We
+    save the reading time when running the backfill pipelines. We set a softer
+    threshold to allow flexibility in data delivery.
 
     Parameters
     ----------

From 1873280b8f599f4a87a92e63cc83417ac8ee9d65 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <31444565+jingjtang@users.noreply.github.com>
Date: Tue, 30 Aug 2022 20:13:29 -0400
Subject: [PATCH 16/20] Turn off index arg

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>
---
 quidel_covidtest/delphi_quidel_covidtest/backfill.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
index 65963612e..cbc01e412 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/backfill.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -112,7 +112,7 @@ def get_date(file_link):
     path = backfill_dir + "/quidel_covidtest_from_%s_to_%s.parquet"%(
         datetime.strftime(earliest_date, "%Y%m%d"),
         datetime.strftime(latest_date, "%Y%m%d"))
-    merged_file.to_parquet(path)
+    merged_file.to_parquet(path, index=False)
 
     # Delete daily files once we have the merged one.
     if not test_mode:

From 9fd95aba25377b85d1cad7b94f6c9df158e50143 Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Wed, 31 Aug 2022 21:15:40 -0400
Subject: [PATCH 17/20] remove index arg when saving parquet files; add
 state_id for backfill

---
 quidel_covidtest/delphi_quidel_covidtest/backfill.py | 6 ++++--
 quidel_covidtest/delphi_quidel_covidtest/pull.py     | 4 +---
 quidel_covidtest/tests/test_backfill.py              | 2 +-
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
index cbc01e412..c594bd3c7 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/backfill.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -26,6 +26,8 @@ def store_backfill_file(df, _end_date, backfill_dir):
     backfilldata = df.copy()
     backfilldata = gmpr.replace_geocode(backfilldata, from_code="zip", new_code="fips",
                           from_col="zip", new_col="fips", date_col="timestamp")
+    backfilldata = gmpr.add_geocode(backfilldata, from_code="fips", new_code="state_id",
+                          from_col="fips", new_col="state_id")
     backfilldata.rename({"timestamp": "time_value",
                          "totalTest_total": "den_total",
                          "positiveTest_total": "num_total",
@@ -44,7 +46,7 @@ def store_backfill_file(df, _end_date, backfill_dir):
                         axis=1, inplace=True)
     #Store one year's backfill data
     _start_date = _end_date.replace(year=_end_date.year-1)
-    selected_columns = ['time_value', 'fips',
+    selected_columns = ['time_value', 'fips', 'state_id',
                         'den_total', 'num_total',
                         'num_age_0_4', 'den_age_0_4',
                         'num_age_5_17', 'den_age_5_17',
@@ -57,7 +59,7 @@ def store_backfill_file(df, _end_date, backfill_dir):
     path = backfill_dir + \
         "/quidel_covidtest_as_of_%s.parquet"%datetime.strftime(_end_date, "%Y%m%d")
     # Store intermediate file into the backfill folder
-    backfilldata.to_parquet(path)
+    backfilldata.to_parquet(path, index=False)
 
 def merge_backfill_file(backfill_dir, backfill_merge_day, today,
                         test_mode=False, check_nd=25):
diff --git a/quidel_covidtest/delphi_quidel_covidtest/pull.py b/quidel_covidtest/delphi_quidel_covidtest/pull.py
index c2357b64b..2ac5b958f 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/pull.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/pull.py
@@ -8,11 +8,9 @@
 import pandas as pd
 import numpy as np
 
-from delphi_utils import GeoMapper
-
 from .constants import AGE_GROUPS
 
-gmpr = GeoMapper()
+
 
 def get_from_s3(start_date, end_date, bucket, logger):
     """
diff --git a/quidel_covidtest/tests/test_backfill.py b/quidel_covidtest/tests/test_backfill.py
index 35d82bf12..4dbe7c70c 100644
--- a/quidel_covidtest/tests/test_backfill.py
+++ b/quidel_covidtest/tests/test_backfill.py
@@ -41,7 +41,7 @@ def test_store_backfill_file(self):
         
         backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')
         
-        selected_columns = ['time_value', 'fips',
+        selected_columns = ['time_value', 'fips', 'state_id',
                         'den_total', 'num_total',
                         'num_age_0_4', 'den_age_0_4',
                         'num_age_5_17', 'den_age_5_17',

From 4ea503e8df6da5a58b4dd9fc7fa2a2b69ec361dd Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Wed, 31 Aug 2022 21:17:55 -0400
Subject: [PATCH 18/20] update test backfill files

---
 .../quidel_covidtest_as_of_20200817.parquet   | Bin 13610 -> 13042 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet b/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet
index 0e730fd5a928c983f46722abc431f27e34e95e08..2b9a6ffa7c8bdd02cce4a66169cd791881e6bee3 100644
GIT binary patch
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From 4846e4c2551bf5ea48790b136ab553a41e8df7bf Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Tue, 6 Sep 2022 15:00:04 -0400
Subject: [PATCH 19/20] remove backfill test files

---
 .../quidel_covidtest_as_of_20200817.parquet     | Bin 13042 -> 0 bytes
 .../quidel_covidtest_as_of_20200818.parquet     | Bin 13603 -> 0 bytes
 .../quidel_covidtest_as_of_20200819.parquet     | Bin 13603 -> 0 bytes
 .../quidel_covidtest_as_of_20200820.parquet     | Bin 13603 -> 0 bytes
 4 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet
 delete mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200818.parquet
 delete mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200819.parquet
 delete mode 100644 quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200820.parquet

diff --git a/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet b/quidel_covidtest/tests/backfill/quidel_covidtest_as_of_20200817.parquet
deleted file mode 100644
index 2b9a6ffa7c8bdd02cce4a66169cd791881e6bee3..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 5bf0933fa41603dc6745049797cb9a61fd95810d Mon Sep 17 00:00:00 2001
From: Jingjing Tang <jingjingtang@Jingjings-MacBook-Pro.local>
Date: Tue, 6 Sep 2022 15:00:29 -0400
Subject: [PATCH 20/20] add cases when there is no daily file stored

---
 .../delphi_quidel_covidtest/backfill.py       |  2 ++
 quidel_covidtest/tests/test_backfill.py       | 28 +++++++++++++++----
 2 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/quidel_covidtest/delphi_quidel_covidtest/backfill.py b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
index c594bd3c7..7e8482551 100644
--- a/quidel_covidtest/delphi_quidel_covidtest/backfill.py
+++ b/quidel_covidtest/delphi_quidel_covidtest/backfill.py
@@ -86,6 +86,8 @@ def merge_backfill_file(backfill_dir, backfill_merge_day, today,
         considerations
     """
     new_files = glob.glob(backfill_dir + "/quidel_covidtest_as_of_*")
+    if len(new_files) == 0: # if no any daily file is stored
+        return
 
     def get_date(file_link):
         # Keep the function here consistent with the backfill path in
diff --git a/quidel_covidtest/tests/test_backfill.py b/quidel_covidtest/tests/test_backfill.py
index 4dbe7c70c..7a033fb47 100644
--- a/quidel_covidtest/tests/test_backfill.py
+++ b/quidel_covidtest/tests/test_backfill.py
@@ -17,9 +17,8 @@
 backfill_dir="./backfill"
 
 class TestBackfill:
-        
-    def test_store_backfill_file(self):
-        df, _end_date = pull_quidel_covidtest({
+    
+    df, _end_date = pull_quidel_covidtest({
             "static_file_dir": "../static",
             "input_cache_dir": "./cache",
             "export_start_date": "2020-06-30",
@@ -34,8 +33,10 @@ def test_store_backfill_file(self):
             "wip_signal": "",
             "test_mode": True
         }, TEST_LOGGER)
-        
-        store_backfill_file(df, datetime(2020, 1, 1), backfill_dir)
+    
+    def test_store_backfill_file(self):
+                
+        store_backfill_file(self.df, datetime(2020, 1, 1), backfill_dir)
         fn = "quidel_covidtest_as_of_20200101.parquet"
         assert fn in os.listdir(backfill_dir)
         
@@ -57,10 +58,18 @@ def test_store_backfill_file(self):
     def test_merge_backfill_file(self):
         
         today = datetime.today()
-        new_files = glob.glob(backfill_dir + "/*.parquet")
         fn = "quidel_covidtest_from_20200817_to_20200820.parquet"
         assert fn not in os.listdir(backfill_dir)
         
+        # Check the when no daily file stored
+        today = datetime(2020, 8, 20)
+        merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=8)
+        assert fn not in os.listdir(backfill_dir)
+        
+        for d in range(17, 21):
+            dropdate = datetime(2020, 8, d)        
+            store_backfill_file(self.df, dropdate, backfill_dir)
+                
         # Check the when the merged file is not generated
         today = datetime(2020, 8, 20)
         merge_backfill_file(backfill_dir, today.weekday(), today, test_mode=True, check_nd=8)
@@ -71,13 +80,20 @@ def test_merge_backfill_file(self):
         assert fn in os.listdir(backfill_dir)
 
         # Read daily file
+        new_files = glob.glob(backfill_dir + "/quidel_covidtest*.parquet")
         pdList = []        
         for file in new_files:
+            if "from" in file:
+                continue
             df = pd.read_parquet(file, engine='pyarrow')
             issue_date = datetime.strptime(file[-16:-8], "%Y%m%d")
             df["issue_date"] = issue_date
             df["lag"] = [(issue_date - x).days for x in df["time_value"]]
             pdList.append(df)
+            os.remove(file)
+        new_files = glob.glob(backfill_dir + "/quidel_covidtest*.parquet")
+        assert len(new_files) == 1
+        
         expected = pd.concat(pdList).sort_values(["time_value", "fips"])
         
         # Read the merged file