Merge branch 'main' into nans_covidactnow

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.16
+current_version = 0.1.25
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

.github/workflows/r-ci.yml

@@ -48,14 +48,12 @@ jobs:
             ${{ runner.os }}-r-facebook-survey-
       - name: Install R dependencies
         run: |
-          if ( packageVersion("readr") != "1.4.0" ) {
-            install.packages("devtools")
-            devtools::install_version("readr", version = "1.4.0")
+          if ( !require("remotes") ) {
+            install.packages("remotes")
           }
-          install.packages("remotes")
-          remotes::update_packages(c("rcmdcheck", "mockr"), upgrade="always")
+          remotes::update_packages(c("rcmdcheck", "mockr", "remotes"), upgrade="always")
           dependency_list <- remotes::dev_package_deps(dependencies=TRUE)
-          remotes::update_packages(dependency_list$package[dependency_list$package != "readr"], upgrade="always")
+          remotes::update_packages(dependency_list$package, upgrade="always")
         shell: Rscript {0}
       - name: Check
         run: |

.gitignore

@@ -4,7 +4,7 @@
 params.json
 
 # Do not commit output files
-receiving/*.csv
+**/receiving/*.csv
 
 # Do not commit hidden macOS files
 .DS_Store

_delphi_utils_python/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.12
+current_version = 0.1.17
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_delphi_utils_python/delphi_utils/__init__.py

@@ -14,4 +14,4 @@
 from .signal import add_prefix
 from .nancodes import Nans
 
-__version__ = "0.1.12"
+__version__ = "0.1.17"

_delphi_utils_python/delphi_utils/archive.py

@@ -105,7 +105,8 @@ def diff_export_csv(
     # Code deleted entries as nans with the deleted missing code
     deleted_df = before_df.loc[deleted_idx, :].copy()
     deleted_df[["val", "se", "sample_size"]] = np.nan
-    deleted_df[["missing_val", "missing_se", "missing_sample_size"]] = Nans.DELETED
+    if "missing_val" in after_df_cmn.columns:
+        deleted_df[["missing_val", "missing_se", "missing_sample_size"]] = Nans.DELETED
 
     return (
         deleted_df,
@@ -254,26 +255,7 @@ def diff_exports(self) -> Tuple[Files, FileDiffMap, Files]:
                 new_issues_df.to_csv(diff_file, na_rep="NA")
                 common_diffs[after_file] = diff_file
 
-        export_csv_dtypes = {
-            "geo_id": str, "val": float, "se": float, "sample_size": float,
-            "missing_val": int, "missing_se": int, "missing_sample_size": int
-        }
-
-        # Replace deleted files with empty versions, but only if the cached version is not
-        # already empty
-        deleted_files_nanfilled = []
-        for deleted_file in deleted_files:
-            deleted_df = pd.read_csv(deleted_file, dtype=export_csv_dtypes)
-            print(
-                f"Diff deleted {deleted_file}; generating corresponding CSV with deleted rows."
-            )
-            deleted_df[["val", "se", "sample_size"]] = np.nan
-            deleted_df[["missing_val", "missing_se", "missing_sample_size"]] = Nans.DELETED
-            filename = join(self.export_dir, basename(deleted_file))
-            deleted_df.to_csv(filename, index=False)
-            deleted_files_nanfilled.append(filename)
-
-        return deleted_files_nanfilled, common_diffs, new_files
+        return deleted_files, common_diffs, new_files
 
     def archive_exports(self, exported_files: Files) -> Tuple[Files, Files]:
         """
@@ -299,10 +281,9 @@ def filter_exports(self, common_diffs: FileDiffMap):
         Filter export directory to only contain relevant files.
 
         Filters down the export_dir to only contain:
-        1) New files, 2) Changed files, filtered-down to the ADDED and CHANGED rows
-        only, and 3) Deleted files replaced with empty CSVs with the same name. Should
-        be called after archive_exports() so we archive the raw exports before potentially
-        modifying them.
+        1) New files, 2) Changed files, filtered-down to the ADDED and CHANGED rows only.
+        Should be called after archive_exports() so we archive the raw exports before
+        potentially modifying them.
 
         Parameters
         ----------
@@ -331,13 +312,12 @@ def run(self):
         self.update_cache()
 
         # Diff exports, and make incremental versions
-        deleted_files, common_diffs, new_files = self.diff_exports()
+        _, common_diffs, new_files = self.diff_exports()
 
-        # Archive changed, new, and emptied deleted files
+        # Archive changed and new files only
         to_archive = [f for f, diff in common_diffs.items()
                       if diff is not None]
         to_archive += new_files
-        to_archive += deleted_files
         _, fails = self.archive_exports(to_archive)
 
         # Filter existing exports to exclude those that failed to archive

_delphi_utils_python/delphi_utils/export.py

@@ -5,6 +5,7 @@
 from typing import Optional
 import logging
 
+from epiweeks import Week
 import numpy as np
 import pandas as pd
 
@@ -39,7 +40,8 @@ def create_export_csv(
     end_date: Optional[datetime] = None,
     remove_null_samples: Optional[bool] = False,
     write_empty_days: Optional[bool] = False,
-    logger: Optional[logging.Logger] = None
+    logger: Optional[logging.Logger] = None,
+    weekly_dates = False,
 ):
     """Export data in the format expected by the Delphi API.
 
@@ -68,6 +70,9 @@ def create_export_csv(
         even if there is no data for the day. If false, only the days present are written.
     logger: Optional[logging.Logger]
         Pass a logger object here to log information about contradictory missing codes.
+    weekly_dates: Optional[bool]
+        Whether the output data are weekly or not. If True, will prefix files with
+        "weekly_YYYYWW" where WW is the epiweek instead of the usual YYYYMMDD for daily files.
 
     Returns
     ---------
@@ -90,10 +95,15 @@ def create_export_csv(
         dates = pd.date_range(start_date, end_date)
 
     for date in dates:
+        if weekly_dates:
+            t = Week.fromdate(pd.to_datetime(str(date)))
+            date_str = "weekly_" + str(t.year) + str(t.week).zfill(2)
+        else:
+            date_str = date.strftime('%Y%m%d')
         if metric is None:
-            export_filename = f"{date.strftime('%Y%m%d')}_{geo_res}_{sensor}.csv"
+            export_filename = f"{date_str}_{geo_res}_{sensor}.csv"
         else:
-            export_filename = f"{date.strftime('%Y%m%d')}_{geo_res}_{metric}_{sensor}.csv"
+            export_filename = f"{date_str}_{geo_res}_{metric}_{sensor}.csv"
         export_file = join(export_dir, export_filename)
         expected_columns = [
             "geo_id",

_delphi_utils_python/delphi_utils/geomap.py

@@ -183,7 +183,7 @@ def megacounty_creation(
         thr_win_len,
         thr_col="visits",
         fips_col="fips",
-        date_col="date",
+        date_col="timestamp",
         mega_col="megafips",
     ):
         """Create megacounty column.
@@ -340,7 +340,7 @@ def replace_geocode(
         new_code,
         from_col=None,
         new_col=None,
-        date_col="date",
+        date_col="timestamp",
         data_cols=None,
         dropna=True,
     ):
@@ -366,7 +366,7 @@ def replace_geocode(
         new_code: {'fips', 'zip', 'state_code', 'state_id', 'state_name', 'hrr', 'msa',
                    'hhs'}
             Specifies the geocode type of the data in new_col.
-        date_col: str or None, default "date"
+        date_col: str or None, default "timestamp"
             Specify which column contains the date values. Used for value aggregation.
             If None, then the aggregation is done only on geo_id.
         data_cols: list, default None
@@ -457,7 +457,7 @@ def fips_to_megacounty(
         thr_win_len,
         thr_col="visits",
         fips_col="fips",
-        date_col="date",
+        date_col="timestamp",
         mega_col="megafips",
         count_cols=None,
     ):

_delphi_utils_python/delphi_utils/runner.py

@@ -4,7 +4,7 @@
 from typing import Any, Callable, Dict, Optional
 from .archive import ArchiveDiffer, archiver_from_params
 from .logger import get_structured_logger
-from .utils import read_params
+from .utils import read_params, transfer_files
 from .validator.validate import Validator
 from .validator.run import validator_from_params
 
@@ -44,8 +44,11 @@ def run_indicator_pipeline(indicator_fn:  Callable[[Params], None],
         validation_report.log(get_structured_logger(
             name = indicator_fn.__module__,
             filename=params["common"].get("log_filename", None)))
-    if archiver and (not validator or validation_report.success()):
-        archiver.run()
+    if (not validator or validation_report.success()):
+        if archiver:
+            archiver.run()
+        if "delivery" in params:
+            transfer_files()
 
 
 if __name__ == "__main__":

_delphi_utils_python/delphi_utils/utils.py

@@ -1,8 +1,8 @@
 """Read parameter files containing configuration information."""
 # -*- coding: utf-8 -*-
 from json import load,dump
-from os.path import exists
-from shutil import copyfile
+from shutil import copyfile, move
+import os
 import sys
 
 def read_params():
@@ -11,7 +11,7 @@ def read_params():
     If the file does not exist, it copies the file 'params.json.template' to
     'params.json' and then reads the file.
     """
-    if not exists("params.json"):
+    if not os.path.exists("params.json"):
         copyfile("params.json.template", "params.json")
 
     with open("params.json", "r") as json_file:
@@ -87,3 +87,13 @@ def params_run():
         with open("params.json", "w") as f:
             dump(params, f, sort_keys=True, indent=2)
         print(f"Updated {n} items")
+
+def transfer_files():
+    """Transfer files to prepare for acquisition."""
+    params = read_params()
+    export_dir = params["common"].get("export_dir", None)
+    delivery_dir = params["delivery"].get("delivery_dir", None)
+    files_to_export = os.listdir(export_dir)
+    for file_name in files_to_export:
+        if file_name.endswith(".csv") or file_name.endswith(".CSV"):
+            move(os.path.join(export_dir, file_name), delivery_dir)

_delphi_utils_python/setup.py

@@ -7,6 +7,7 @@
 required = [
     "boto3",
     "covidcast",
+    "epiweeks",
     "freezegun",
     "gitpython",
     "mock",
@@ -24,7 +25,7 @@
 
 setup(
     name="delphi_utils",
-    version="0.1.12",
+    version="0.1.17",
     description="Shared Utility Functions for Indicators",
     long_description=long_description,
     long_description_content_type="text/markdown",
@@ -35,7 +36,7 @@
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Developers",
-        "Programming Language :: Python :: 3.7",
+        "Programming Language :: Python :: 3.8",
     ],
     packages=find_packages(),
     package_data={'': ['data/*.csv']}