fix: concurrency file order TDE-1213 (#998)

#### Motivation

When supplying multiple source locations to use for standardising, if
there are overlapping source images, the VRT created does not honour the
priority order for the supplied datasets. This Pull Request is to retain
the priority of the images for merging.

#### Modification

Move away from using `as_completed` for parallel processing so that the
output file list is in the same order as the input file list.

#### Checklist

_If not applicable, provide explanation of why._

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

scripts/files/fs.py

@@ -1,5 +1,5 @@
 import os
-from concurrent.futures import Future, ThreadPoolExecutor, as_completed
+from concurrent.futures import Future, ThreadPoolExecutor
 from datetime import datetime
 from pathlib import Path
 from typing import TYPE_CHECKING
@@ -105,14 +105,17 @@ def write_all(inputs: list[str], target: str, concurrency: int | None = 4, gener
     Returns:
         list of written file paths
     """
+    results: list[Future] = []  # type: ignore
     written_tiffs: list[str] = []
     with ThreadPoolExecutor(max_workers=concurrency) as executor:
-        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())
-            else:
-                written_tiffs.append(future.result())
+        for input_ in inputs:
+            results.append(executor.submit(write_file, input_, target, generate_name))
+
+    for future in results:
+        if future.exception():
+            get_log().warn("Failed Read-Write", error=future.exception())
+        else:
+            written_tiffs.append(future.result())
 
     if len(inputs) != len(written_tiffs):
         get_log().error("Missing Files", count=len(inputs) - len(written_tiffs))
@@ -130,26 +133,28 @@ def write_sidecars(inputs: list[str], target: str, concurrency: int | None = 4)
         target: target folder to write to
         concurrency: max thread pool workers
     """
+    results: list[Future] = []  # type: ignore
     with ThreadPoolExecutor(max_workers=concurrency) as executor:
-        results = {write_file(executor, input_, target): input_ for input_ in inputs}
-        for future in as_completed(results):
-            future_ex = future.exception()
-            if isinstance(future_ex, NoSuchFileError):
-                get_log().info("No sidecar file found; skipping", path=future_ex.path)
-            else:
-                get_log().info("wrote_sidecar_file", path=future.result())
+        for input_ in inputs:
+            results.append(executor.submit(write_file, input_, target))
+
+    for future in results:
+        future_ex = future.exception()
+        if isinstance(future_ex, NoSuchFileError):
+            get_log().info("No sidecar file found; skipping", error=future.exception())
+        else:
+            get_log().info("wrote_sidecar_file", path=future.result())
 
 
-def write_file(executor: ThreadPoolExecutor, input_: str, target: str, generate_name: bool | None = True) -> Future[str]:
+def write_file(input_: str, target: str, generate_name: bool | None = True) -> 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.
+        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.
+        str: Target file name.
     """
     get_log().info(f"Trying write from file: {input_}")
 
@@ -159,12 +164,7 @@ def write_file(executor: ThreadPoolExecutor, input_: str, target: str, generate_
     else:
         target_file_name = os.path.basename(input_)
 
-    try:
-        return executor.submit(copy, input_, os.path.join(target, target_file_name))
-    except NoSuchFileError as nsfe:
-        future: Future[str] = Future()
-        future.set_exception(nsfe)
-        return future
+    return copy(input_, os.path.join(target, target_file_name))
 
 
 class NoSuchFileError(Exception):

scripts/files/tests/fs_test.py

@@ -89,6 +89,22 @@ def test_write_sidecars_one_found(capsys: CaptureFixture[str], subtests: SubTest
     rmtree(target)
 
 
+def test_write_all_in_order(setup: str) -> None:
+    inputs: list[str] = []
+    file_contents = "a" * 1000 * 1000
+    i = 0
+    while i < 10:
+        path = Path(os.path.join(setup, str(i)))
+        if i % 2 == 0:
+            path.write_text(file_contents, encoding="utf-8")  # 1MB
+        else:
+            path.touch()
+        inputs.append(path.as_posix())
+        i += 1
+    written_files = write_all(inputs=inputs, target=setup, generate_name=False)
+    assert written_files == inputs
+
+
 @mock_aws
 def test_should_get_s3_object_modified_datetime() -> None:
     bucket_name = "any-bucket-name"