Merge pull request #177 from kbase/develop

Release v1.3.5

Author: MrCreosote

RELEASE_NOTES.md

@@ -1,3 +1,6 @@
+### Version 1.3.5
+- Fixed a bug that under some circumstances could cause incomplete file metadata to be returned.
+
 ### Version 1.3.4
 - Alter the behavior of the bulk specification file writers to return an error if the
   input `types` parameter is empty.

staging_service/app.py

@@ -34,7 +34,7 @@
 
 logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
 routes = web.RouteTableDef()
-VERSION = "1.3.4"
+VERSION = "1.3.5"
 
 _DATATYPE_MAPPINGS = None
 

staging_service/metadata.py

@@ -48,7 +48,8 @@ async def _generate_metadata(path: Path, source: str):
     else:
         data = {}
     # first ouptut of md5sum is the checksum
-    data["source"] = source
+    if source:
+        data["source"] = source
     try:
         md5 = hashlib.md5(open(path.full_path, "rb").read()).hexdigest()
     except:
@@ -165,7 +166,7 @@ async def some_metadata(path: Path, desired_fields=False, source=None):
         os.stat(path.metadata_path).st_mtime < file_stats["mtime"] / 1000
     ):
         # if metadata  does not exist or older than file: regenerate
-        if source is None:
+        if source is None:  # TODO BUGFIX this will overwrite any source in the file
             source = _determine_source(path)
         data = await _generate_metadata(path, source)
     else:  # metadata already exists and is up to date
@@ -174,9 +175,11 @@ async def some_metadata(path: Path, desired_fields=False, source=None):
             data = await f.read()
             data = decoder.decode(data)
         # due to legacy code, some file has corrupted metadata file
+        # Also if a file is listed or checked for existence before the upload completes
+        # this code block will be triggered
         expected_keys = ["source", "md5", "lineCount", "head", "tail"]
-        if set(expected_keys) > set(data.keys()):
-            if source is None:
+        if not set(expected_keys) <= set(data.keys()):
+            if source is None and "source" not in data:
                 source = _determine_source(path)
             data = await _generate_metadata(path, source)
     data = {**data, **file_stats}

tests/test_metadata.py

@@ -0,0 +1,80 @@
+""" Unit tests for the metadata handling routines. """
+
+import json
+import uuid
+
+from collections.abc import Generator
+from pathlib import Path as PyPath
+from pytest import fixture
+
+from staging_service.utils import Path
+from staging_service.metadata import some_metadata
+
+from tests.test_app import FileUtil
+
+# TODO TEST add more unit tests here.
+
+
+@fixture(scope="module")
+def temp_dir() -> Generator[PyPath, None, None]:
+    with FileUtil() as fu:
+        childdir = PyPath(fu.make_dir(str(uuid.uuid4()))).resolve()
+
+        yield childdir
+
+    # FileUtil will auto delete after exiting
+
+
+async def test_incomplete_metadata_file_update(temp_dir: Path):
+    """
+    Tests the case where a file is listed or checked for existance prior to completing
+    upload, and then an UPA is added to the file. This previously caused incomplete metadata
+    to be returned as the logic for whether to run the metadata regeneration code based on
+    the contents of the current metadata file was incorrect.
+    See https://kbase-jira.atlassian.net/browse/PTV-1767
+    """
+    await _incomplete_metadata_file_update(
+        temp_dir,
+        {"source": "some place", "UPA": "1/2/3"},
+        "some place"
+        )
+
+    await _incomplete_metadata_file_update(
+        temp_dir,
+        {"UPA": "1/2/3"},
+        "Unknown"
+        )
+
+async def _incomplete_metadata_file_update(temp_dir, metadict, source):
+    target = Path(
+        str(temp_dir / "full"),
+        str(temp_dir / "meta"),
+        "user_path",
+        "myfilename",
+        "super_fake_jgi_path")
+
+    with open(target.full_path, "w") as p:
+        p.writelines(make_test_lines(1, 6))
+    with open(target.metadata_path, "w") as p:
+        p.write(json.dumps(metadict))
+
+    res = await some_metadata(target)
+
+    assert "mtime" in res  # just check the file time is there
+    del res["mtime"]
+
+    assert res == {
+        "source": source,
+        "md5": "9f07da9655223b777121141ff7735f25",
+        "head": "".join(make_test_lines(1, 5)),
+        "tail": "".join(make_test_lines(2, 6)),
+        "UPA": "1/2/3",
+        "isFolder": False,
+        "lineCount": "5",
+        "name": "myfilename",
+        "path": "user_path",
+        "size": 1280
+        }
+
+def make_test_lines(start, stop):
+    return [str(i) + "a" * (256 - len(str(i)) - 1) + "\n" for i in range(start, stop)]