Fix JHU bug that renamed fips to county in receiving

_delphi_utils_python/delphi_utils/archive.py

@@ -25,6 +25,7 @@
 Created: 2020-08-06
 """
 
+from argparse import ArgumentParser
 from contextlib import contextmanager
 import filecmp
 from glob import glob
@@ -39,9 +40,12 @@
 from git.refs.head import Head
 import pandas as pd
 
+from .utils import read_params
+
 Files = List[str]
 FileDiffMap = Dict[str, Optional[str]]
 
+
 def diff_export_csv(
     before_csv: str,
     after_csv: str
@@ -65,7 +69,8 @@ def diff_export_csv(
         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}
 
     before_df = pd.read_csv(before_csv, dtype=export_csv_dtypes)
     before_df.set_index("geo_id", inplace=True)
@@ -89,6 +94,42 @@ def diff_export_csv(
         after_df_cmn.loc[~(same_mask.all(axis=1)), :],
         after_df.loc[added_idx, :])
 
+
+def run_module(archive_type: str,
+               cache_dir: str,
+               export_dir: str,
+               **kwargs):
+    """Builds and runs an ArchiveDiffer.
+
+    Parameters
+    ----------
+    archive_type: str
+        Type of ArchiveDiffer to run.  Must be one of ["git", "s3"] which correspond to `GitArchiveDiffer` and `S3ArchiveDiffer`, respectively.
+    cache_dir: str
+        The directory for storing most recent archived/uploaded CSVs to start diffing from.
+    export_dir: str
+        The directory with most recent exported CSVs to diff to.
+    **kwargs:
+        Keyword arguments corresponding to constructor arguments for the respective ArchiveDiffers.
+    """
+    if archive_type == "git":
+        arch_diff = GitArchiveDiffer(cache_dir,
+                                     export_dir,
+                                     kwargs["branch_name"],
+                                     kwargs["override_dirty"],
+                                     kwargs["commit_partial_success"],
+                                     kwargs["commit_message"])
+    elif archive_type == "s3":
+        arch_diff = S3ArchiveDiffer(cache_dir,
+                                    export_dir,
+                                    kwargs["bucket_name"],
+                                    kwargs["indicator_prefix"],
+                                    kwargs["aws_credentials"])
+    else:
+        raise ValueError(f"No archive type named '{archive_type}'")
+    arch_diff.run()
+
+
 class ArchiveDiffer:
     """
     Base class for performing diffing and archiving of exported covidcast CSVs
@@ -140,12 +181,16 @@ def diff_exports(self) -> Tuple[Files, FileDiffMap, Files]:
         assert self._cache_updated
 
         # Glob to only pick out CSV files, ignore hidden files
-        previous_files = set(basename(f) for f in glob(join(self.cache_dir, "*.csv")))
-        exported_files = set(basename(f) for f in glob(join(self.export_dir, "*.csv")))
+        previous_files = set(basename(f)
+                             for f in glob(join(self.cache_dir, "*.csv")))
+        exported_files = set(basename(f)
+                             for f in glob(join(self.export_dir, "*.csv")))
 
-        deleted_files = sorted(join(self.cache_dir, f) for f in previous_files - exported_files)
+        deleted_files = sorted(join(self.cache_dir, f)
+                               for f in previous_files - exported_files)
         common_filenames = sorted(exported_files & previous_files)
-        new_files = sorted(join(self.export_dir, f) for f in exported_files - previous_files)
+        new_files = sorted(join(self.export_dir, f)
+                           for f in exported_files - previous_files)
 
         common_diffs: Dict[str, Optional[str]] = {}
         for filename in common_filenames:
@@ -158,11 +203,13 @@ def diff_exports(self) -> Tuple[Files, FileDiffMap, Files]:
             if filecmp.cmp(before_file, after_file, shallow=False):
                 continue
 
-            deleted_df, changed_df, added_df = diff_export_csv(before_file, after_file)
+            deleted_df, changed_df, added_df = diff_export_csv(
+                before_file, after_file)
             new_issues_df = pd.concat([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")
+                print(
+                    f"Warning, diff has deleted indices in {after_file} that will be ignored")
 
             # Write the diffs to diff_file, if applicable
             if len(new_issues_df) > 0:
@@ -220,6 +267,29 @@ def filter_exports(self, common_diffs: FileDiffMap):
             else:
                 replace(diff_file, exported_file)
 
+    def run(self):
+        """Runs the differ and archives the changed and new files."""
+        self.update_cache()
+
+        # Diff exports, and make incremental versions
+        _, common_diffs, new_files = self.diff_exports()
+
+        # 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
+        _, fails = self.archive_exports(to_archive)
+
+        # Filter existing exports to exclude those that failed to archive
+        succ_common_diffs = {f: diff for f,
+                             diff in common_diffs.items() if f not in fails}
+        self.filter_exports(succ_common_diffs)
+
+        # Report failures: someone should probably look at them
+        for exported_file in fails:
+            print(f"Failed to archive '{exported_file}'")
+
+
 class S3ArchiveDiffer(ArchiveDiffer):
     """
     AWS S3 backend for archving
@@ -263,11 +333,14 @@ def update_cache(self):
         For making sure cache_dir is updated with all latest files from the S3 bucket.
         """
         # List all indicator-related objects from S3
-        archive_objects = self.bucket.objects.filter(Prefix=self.indicator_prefix).all()
-        archive_objects = [obj for obj in archive_objects if obj.key.endswith(".csv")]
+        archive_objects = self.bucket.objects.filter(
+            Prefix=self.indicator_prefix).all()
+        archive_objects = [
+            obj for obj in archive_objects if obj.key.endswith(".csv")]
 
         # Check against what we have locally and download missing ones
-        cached_files = set(basename(f) for f in glob(join(self.cache_dir, "*.csv")))
+        cached_files = set(basename(f)
+                           for f in glob(join(self.cache_dir, "*.csv")))
         for obj in archive_objects:
             archive_file = basename(obj.key)
             cached_file = join(self.cache_dir, archive_file)
@@ -297,7 +370,8 @@ def archive_exports(self, exported_files: Files) -> Tuple[Files, Files]:
         archive_fail = []
 
         for exported_file in exported_files:
-            cached_file = abspath(join(self.cache_dir, basename(exported_file)))
+            cached_file = abspath(
+                join(self.cache_dir, basename(exported_file)))
             archive_key = join(self.indicator_prefix, basename(exported_file))
 
             try:
@@ -314,6 +388,7 @@ def archive_exports(self, exported_files: Files) -> Tuple[Files, Files]:
 
         return archive_success, archive_fail
 
+
 class GitArchiveDiffer(ArchiveDiffer):
     """
     Local git repo backend for archiving
@@ -352,7 +427,7 @@ def __init__(
         super().__init__(cache_dir, export_dir)
 
         assert override_dirty or not commit_partial_success, \
-                "Only can commit_partial_success=True when override_dirty=True"
+            "Only can commit_partial_success=True when override_dirty=True"
 
         # Assumes a repository is set up already, will raise exception if not found
         self.repo = Repo(cache_dir, search_parent_directories=True)
@@ -405,7 +480,8 @@ def update_cache(self):
         """
         # Make sure cache directory is clean: has everything nicely committed
         if not self.override_dirty:
-            cache_clean = not self.repo.is_dirty(untracked_files=True, path=abspath(self.cache_dir))
+            cache_clean = not self.repo.is_dirty(
+                untracked_files=True, path=abspath(self.cache_dir))
             assert cache_clean, f"There are uncommitted changes in the cache dir '{self.cache_dir}'"
 
         self._cache_updated = True
@@ -439,11 +515,14 @@ def archive_exports(self, exported_files: Files) -> Tuple[Files, Files]:
         with self.archiving_branch():
             # Abs paths of all modified files to check if we will override uncommitted changes
             working_tree_dir = self.repo.working_tree_dir
-            dirty_files = [join(working_tree_dir, f) for f in self.repo.untracked_files]
-            dirty_files += [join(working_tree_dir, d.a_path) for d in self.repo.index.diff(None)]
+            dirty_files = [join(working_tree_dir, f)
+                           for f in self.repo.untracked_files]
+            dirty_files += [join(working_tree_dir, d.a_path)
+                            for d in self.repo.index.diff(None)]
 
             for exported_file in exported_files:
-                archive_file = abspath(join(self.cache_dir, basename(exported_file)))
+                archive_file = abspath(
+                    join(self.cache_dir, basename(exported_file)))
 
                 # Archive and explicitly stage new export, depending if override
                 if self.override_dirty or archive_file not in dirty_files:
@@ -469,11 +548,46 @@ def archive_exports(self, exported_files: Files) -> Tuple[Files, Files]:
             if len(exported_files) > 0:
 
                 # Support partial success and at least one archive succeeded
-                partial_success = self.commit_partial_success and len(archive_success) > 0
+                partial_success = self.commit_partial_success and len(
+                    archive_success) > 0
 
                 if len(archive_success) == len(exported_files) or partial_success:
                     self.repo.index.commit(message=self.commit_message)
 
         self._exports_archived = True
 
         return archive_success, archive_fail
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser()
+    parser.add_argument("--archive_type", required=True, type=str,
+                        choices=["git", "s3"],
+                        help="Type of archive differ to use.")
+    parser.add_argument("--indicator_prefix", type=str, default="",
+                        help="The prefix for S3 keys related to this indicator."
+                        " Required for `archive_type = 's3'")
+    parser.add_argument("--branch_name", type=str, default="",
+                        help=" Branch to use for `archive_type` = 'git'.")
+    parser.add_argument("--override_dirty", action="store_true",
+                        help="Whether to allow overwriting of untracked &"
+                        " uncommitted changes for `archive_type` = 'git'")
+    parser.add_argument("--commit_partial_success",  action="store_true",
+                        help="Whether to still commit for `archive_type` = "
+                        "'git' even if some files were not archived and "
+                        "staged due to `override_dirty` = False.")
+    parser.add_argument("--commit_message", type=str, default="",
+                        help="Commit message for `archive_type` = 'git'")
+    args = parser.parse_args()
+    params = read_params()
+    run_module(args.archive_type,
+               params.cache_dir,
+               params.export_dir,
+               aws_credentials=params.aws_credentials,
+               branch_name=args.branch_name,
+               bucket_name=params.bucket_name,
+               commit_message=args.commit_message,
+               commit_partial_success=args.commit_partial_success,
+               indicator_prefix=args.indicator_prefix,
+               override_dirty=args.override_dirty
+               )