Add NAN code support to Quidel Covidtest

_delphi_utils_python/delphi_utils/archive.py

@@ -40,9 +40,11 @@
 from git import Repo
 from git.refs.head import Head
 import pandas as pd
+import numpy as np
 
 from .utils import read_params
 from .logger import get_structured_logger
+from .nancodes import Nans
 
 Files = List[str]
 FileDiffMap = Dict[str, Optional[str]]
@@ -73,8 +75,10 @@ def diff_export_csv(
         changed_df is the pd.DataFrame of common rows from after_csv with changed values.
         added_df is the pd.DataFrame of added rows from after_csv.
     """
-    export_csv_dtypes = {"geo_id": str, "val": float,
-                         "se": float, "sample_size": float}
+    export_csv_dtypes = {
+        "geo_id": str, "val": float, "se": float, "sample_size": float,
+        "missing_val": int, "missing_se": int, "missing_sample_size": int
+    }
 
     before_df = pd.read_csv(before_csv, dtype=export_csv_dtypes)
     before_df.set_index("geo_id", inplace=True)
@@ -89,12 +93,22 @@ def diff_export_csv(
     before_df_cmn = before_df.reindex(common_idx)
     after_df_cmn = after_df.reindex(common_idx)
 
-    # Exact comparisons, treating NA == NA as True
-    same_mask = before_df_cmn == after_df_cmn
-    same_mask |= pd.isna(before_df_cmn) & pd.isna(after_df_cmn)
+    # If CSVs have different columns (no missingness), mark all values as new
+    if ("missing_val" in before_df_cmn.columns) ^ ("missing_val" in after_df_cmn.columns):
+        same_mask = after_df_cmn.copy()
+        same_mask.loc[:] = False
+    else:
+        # Exact comparisons, treating NA == NA as True
+        same_mask = before_df_cmn == after_df_cmn
+        same_mask |= pd.isna(before_df_cmn) & pd.isna(after_df_cmn)
+
+    # 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
 
     return (
-        before_df.loc[deleted_idx, :],
+        deleted_df,
         after_df_cmn.loc[~(same_mask.all(axis=1)), :],
         after_df.loc[added_idx, :])
 
@@ -227,11 +241,11 @@ def diff_exports(self) -> Tuple[Files, FileDiffMap, Files]:
 
             deleted_df, changed_df, added_df = diff_export_csv(
                 before_file, after_file)
-            new_issues_df = pd.concat([changed_df, added_df], axis=0)
+            new_issues_df = pd.concat([deleted_df, changed_df, added_df], axis=0)
 
             if len(deleted_df) > 0:
                 print(
-                    f"Warning, diff has deleted indices in {after_file} that will be ignored")
+                    f"Diff has deleted indices in {after_file} that have been coded as nans.")
 
             # Write the diffs to diff_file, if applicable
             if len(new_issues_df) > 0:
@@ -240,7 +254,26 @@ def diff_exports(self) -> Tuple[Files, FileDiffMap, Files]:
                 new_issues_df.to_csv(diff_file, na_rep="NA")
                 common_diffs[after_file] = diff_file
 
-        return deleted_files, common_diffs, new_files
+        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 has deleted {deleted_file}; generating a CSV with corresponding 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
 
     def archive_exports(self, exported_files: Files) -> Tuple[Files, Files]:
         """
@@ -266,9 +299,10 @@ 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.
-        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, 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.
 
         Parameters
         ----------
@@ -297,12 +331,13 @@ def run(self):
         self.update_cache()
 
         # Diff exports, and make incremental versions
-        _, common_diffs, new_files = self.diff_exports()
+        deleted_files, common_diffs, new_files = self.diff_exports()
 
-        # Archive changed and new files only
+        # Archive changed, new, and emptied deleted files
         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
@@ -414,6 +449,9 @@ def archive_exports(self,  # pylint: disable=arguments-differ
                 archive_success.append(exported_file)
             except FileNotFoundError:
                 archive_fail.append(exported_file)
+            except shutil.SameFileError:
+                # no need to copy if the cached file is the same
+                archive_success.append(exported_file)
 
         self._exports_archived = True
 

_delphi_utils_python/delphi_utils/export.py

@@ -3,10 +3,32 @@
 from datetime import datetime
 from os.path import join
 from typing import Optional
+import logging
 
 import numpy as np
 import pandas as pd
 
+from .nancodes import Nans
+
+def filter_contradicting_missing_codes(df, sensor, metric, date, logger=None):
+    """Find values with contradictory missingness codes, filter them, and log."""
+    columns = ["val", "se", "sample_size"]
+    # Get indicies where the XNOR is true (i.e. both are true or both are false).
+    masks = [
+        ~(df[column].isna() ^ df["missing_" + column].eq(Nans.NOT_MISSING))
+        for column in columns
+    ]
+    for mask in masks:
+        if not logger is None and df.loc[mask].size > 0:
+            logger.info(
+                "Filtering contradictory missing code in " +
+                "{0}_{1}_{2}.".format(sensor, metric, date.strftime(format="%Y-%m-%d"))
+            )
+            df = df.loc[~mask]
+        elif logger is None and df.loc[mask].size > 0:
+            df = df.loc[~mask]
+    return df
+
 def create_export_csv(
     df: pd.DataFrame,
     export_dir: str,
@@ -16,7 +38,8 @@ def create_export_csv(
     start_date: Optional[datetime] = None,
     end_date: Optional[datetime] = None,
     remove_null_samples: Optional[bool] = False,
-    write_empty_days: Optional[bool] = False
+    write_empty_days: Optional[bool] = False,
+    logger: Optional[logging.Logger] = None
 ):
     """Export data in the format expected by the Delphi API.
 
@@ -43,6 +66,8 @@ def create_export_csv(
     write_empty_days: Optional[bool]
         If true, every day in between start_date and end_date will have a CSV file written
         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.
 
     Returns
     ---------
@@ -70,7 +95,20 @@ def create_export_csv(
         else:
             export_filename = f"{date.strftime('%Y%m%d')}_{geo_res}_{metric}_{sensor}.csv"
         export_file = join(export_dir, export_filename)
-        export_df = df[df["timestamp"] == date][["geo_id", "val", "se", "sample_size",]]
+        expected_columns = [
+            "geo_id",
+            "val",
+            "se",
+            "sample_size",
+            "missing_val",
+            "missing_se",
+            "missing_sample_size"
+        ]
+        export_df = df[df["timestamp"] == date].filter(items=expected_columns)
+        if "missing_val" in export_df.columns:
+            export_df = filter_contradicting_missing_codes(
+                export_df, sensor, metric, date, logger=logger
+            )
         if remove_null_samples:
             export_df = export_df[export_df["sample_size"].notnull()]
         export_df = export_df.round({"val": 7, "se": 7})