fix: should use unique file names when copying files to standardise T…

…DE-1186 (#974)

Co-authored-by: Alice Fage <[email protected]>

#### Motivation

When a source input contains more than one file with the same name,
standardising script should not overwrite them at the copy but copy them
all.

#### Modification

Generate a filename based on the multihash of the input file original
path

#### Checklist

- [ ] Tests updated
- [x] Docs updated
- [x] Issue linked in Title

scripts/files/fs.py

@@ -9,6 +9,7 @@
 
 from scripts.aws.aws_helper import is_s3
 from scripts.files import fs_local, fs_s3
+from scripts.stac.util.checksum import multihash_as_hex
 
 if TYPE_CHECKING:
     from mypy_boto3_s3 import S3Client
@@ -93,20 +94,22 @@ def modified(path: str, s3_client: Optional[S3Client] = None) -> datetime:
     return fs_local.modified(Path(path))
 
 
-def write_all(inputs: List[str], target: str, concurrency: Optional[int] = 4) -> List[str]:
+def write_all(
+    inputs: List[str], target: str, concurrency: Optional[int] = 4, generate_name: Optional[bool] = True
+) -> List[str]:
     """Writes list of files to target destination using multithreading.
-
     Args:
         inputs: list of files to read
         target: target folder to write to
         concurrency: max thread pool workers
+        generated_name: create a target file name based on multihash the source filename
 
     Returns:
         list of written file paths
     """
     written_tiffs: List[str] = []
     with ThreadPoolExecutor(max_workers=concurrency) as executor:
-        futuress = {write_file(executor, input_, target): input_ for input_ in inputs}
+        futuress = {write_file(executor, input_, target, generate_name): input_ for input_ in inputs}
         for future in as_completed(futuress):
             if future.exception():
                 get_log().warn("Failed Read-Write", error=future.exception())
@@ -121,15 +124,13 @@ def write_all(inputs: List[str], target: str, concurrency: Optional[int] = 4) ->
 
 
 def write_sidecars(inputs: List[str], target: str, concurrency: Optional[int] = 4) -> None:
-    """Writes list of files to target destination using multithreading.
+    """Writes list of files (if found) to target destination using multithreading.
+    The copy of the files have a generated file name (@see `write_file`)
 
     Args:
         inputs: list of files to read
         target: target folder to write to
         concurrency: max thread pool workers
-
-    Returns:
-
     """
     with ThreadPoolExecutor(max_workers=concurrency) as executor:
         results = {write_file(executor, input_, target): input_ for input_ in inputs}
@@ -141,20 +142,27 @@ def write_sidecars(inputs: List[str], target: str, concurrency: Optional[int] =
                 get_log().info("wrote_sidecar_file", path=future.result())
 
 
-def write_file(executor: ThreadPoolExecutor, input_: str, target: str) -> Future[str]:
+def write_file(executor: ThreadPoolExecutor, input_: str, target: str, generate_name: Optional[bool] = True) -> Future[str]:
     """Read a file from a path and write it to a target path.
-
     Args:
         executor: A ThreadPoolExecutor instance.
         input_: A path to a file to read.
         target: A path to write the file to.
+        generate_name: create a target file name based on multihash the source filename
 
     Returns:
         Future[str]: The result of the execution.
     """
     get_log().info(f"Trying write from file: {input_}")
+
+    if generate_name:
+        file_name, file_extension = os.path.splitext(input_)
+        target_file_name = f"{multihash_as_hex(str.encode(file_name))}{file_extension}"
+    else:
+        target_file_name = os.path.basename(input_)
+
     try:
-        return executor.submit(copy, input_, os.path.join(target, f"{os.path.basename(input_)}"))
+        return executor.submit(copy, input_, os.path.join(target, target_file_name))
     except NoSuchFileError as nsfe:
         future: Future[str] = Future()
         future.set_exception(nsfe)

scripts/translate_ascii.py

@@ -51,7 +51,7 @@ def main() -> None:
         p.close()
         p.join()
 
-        write_all(inputs=tiffs, target=arguments.target)
+        write_all(inputs=tiffs, target=arguments.target, generate_name=False)
         get_log().info("ascii file translation complete", duration=time_in_ms() - start_time, count=len(tiffs))
 
         # copy any sidecar files to target