Merge pull request #1698 from cmu-delphi/release/indicators_v0.3.24_utils_v0.3.6

Release covidcast-indicators 0.3.24

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.23
+current_version = 0.3.24
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

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 }}",

quidel_covidtest/delphi_quidel_covidtest/backfill.py

@@ -0,0 +1,125 @@
+# -*- 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 = 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",
+                        "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', 'state_id',
+                        '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, index=False)
+
+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 set a softer
+    threshold to allow flexibility in data delivery.
+
+    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_*")
+    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
+        # 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')
+        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)
+    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, index=False)
+
+    # Delete daily files once we have the merged one.
+    if not test_mode:
+        for fn in new_files:
+            os.remove(fn)
+    return

quidel_covidtest/delphi_quidel_covidtest/pull.py

@@ -10,6 +10,8 @@
 
 from .constants import AGE_GROUPS
 
+
+
 def get_from_s3(start_date, end_date, bucket, logger):
     """
     Get raw data from aws s3 bucket.
@@ -57,6 +59,8 @@ 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)

quidel_covidtest/delphi_quidel_covidtest/run.py

@@ -26,7 +26,7 @@
                    check_export_start_date,
                    check_export_end_date,
                    update_cache_file)
-
+from .backfill import (store_backfill_file, merge_backfill_file)
 
 def log_exit(start_time, stats, logger):
     """Log at program exit."""
@@ -66,6 +66,7 @@ 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
@@ -85,16 +86,24 @@ 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"]
+    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"]
     export_day_range = params["indicator"]["export_day_range"]
 
     # 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
+    # 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(

quidel_covidtest/params.json.template

@@ -7,6 +7,8 @@
   "indicator": {
     "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",

quidel_covidtest/setup.py

@@ -4,6 +4,7 @@
 required = [
     "numpy",
     "pandas",
+    "pyarrow",
     "pydocstyle",
     "pytest",
     "pytest-cov",

quidel_covidtest/tests/backfill/.gitignore

@@ -0,0 +1 @@
+*.csv

quidel_covidtest/tests/test_backfill.py

@@ -0,0 +1,108 @@
+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:
+    
+    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)
+    
+    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)
+        
+        backfill_df = pd.read_parquet(backfill_dir + "/"+ fn, engine='pyarrow')
+        
+        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',
+                        '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()
+        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)
+        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
+        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
+        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]
+        
+        os.remove(backfill_dir + "/" + fn)
+        assert fn not in os.listdir(backfill_dir)
+        

quidel_covidtest/tests/test_pull.py

@@ -103,3 +103,4 @@ def test_check_export_start_date(self):
         expected = [datetime(2020, 5, 26), datetime(2020, 6, 20), datetime(2020, 5, 26)]
 
         assert tested == expected
+        

quidel_covidtest/tests/test_run.py

@@ -21,6 +21,8 @@ class TestRun:
         "indicator": {
             "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",