From 27c80dce7ad9349e8ae8788984b1525c2478d575 Mon Sep 17 00:00:00 2001 From: Jermiah Joseph <44614774+jjjermiah@users.noreply.github.com> Date: Mon, 19 Aug 2024 05:42:47 -0400 Subject: [PATCH] fix: fixing the directory() issue due to uploading the local_prefix instead of GCS prefix. (#41) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit first contribution here. Think I found the error. This works for my test Snakefile: ``` rule all: input: "data/done.txt", "data2/done.txt" rule get_directories: input: expand( "data/{directory}", directory = ["a", "b", "c"] ), output: touch("data/done.txt") rule make_a_directory: output: directory("data/{directory}") shell: """ mkdir -p {output} touch {output}/test.txt """ rule get_files: input: expand( "data2/{directory}.txt", directory = ["a", "b", "c"] ) output: touch("data2/done.txt") rule make_a_file: output: "data2/{directory}.txt" shell: """ mkdir -p $(dirname {output}) touch {output} """ ``` I also tried to add another test case which seems to work. I see that the test suites in the storage plugins use `testClasses`. Would adding actual snakefiles and a script to run them also help or does that not follow the plugin standards? ## Summary by CodeRabbit - **New Features** - Introduced new methods for managing Google Cloud Storage: `ensure_bucket_exists` and `upload_directory`. - Added a test case for handling non-empty directories. - **Bug Fixes** - Enhanced the deletion process for directories in Google Cloud Storage. - **Chores** - Created a `.gitignore` file to improve repository cleanliness by excluding unnecessary files. - Updated GitHub Actions CI configuration for improved test output visibility. - **Tests** - Enhanced test suite with additional debugging output and a focus on file operations. --------- Co-authored-by: Johannes Köster --- .github/workflows/ci.yml | 2 +- .gitignore | 17 + poetry.lock | 1042 ++++++++++++---------- snakemake_storage_plugin_gcs/__init__.py | 82 +- tests/test_fake_gcs.py | 2 +- tests/tests.py | 39 +- 6 files changed, 662 insertions(+), 522 deletions(-) create mode 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description = "This package provides a stable interface for interactions between Snakemake and its executor plugins." optional = false -python-versions = ">=3.11,<4.0" +python-versions = "<4.0,>=3.11" files = [ - {file = "snakemake_interface_executor_plugins-8.1.0-py3-none-any.whl", hash = "sha256:180da92e8ff10ed05c26eb2ddb66fd1083a29c0fca72916d9edef578f8406e6b"}, - {file = "snakemake_interface_executor_plugins-8.1.0.tar.gz", hash = "sha256:5c22d2ada03a7cfe81841488c25ebfc8c392e41fdb6819c1158c7a8cd97c0c37"}, + {file = "snakemake_interface_executor_plugins-9.2.0-py3-none-any.whl", hash = "sha256:79caf50998e65e9418acd813d16e9218bf0ec7b2121925a45d9fb6afaf9d8057"}, + {file = "snakemake_interface_executor_plugins-9.2.0.tar.gz", hash = "sha256:67feaf438a0b8b041ec5f1a1dd859f729036c70c07c9fdad895135f5b949e40a"}, ] [package.dependencies] @@ -1484,15 +1543,29 @@ argparse-dataclass = ">=2.0.0,<3.0.0" snakemake-interface-common = ">=1.12.0,<2.0.0" throttler = ">=1.2.2,<2.0.0" +[[package]] +name = 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google.cloud.exceptions from google.cloud import storage from google.api_core import retry @@ -266,6 +268,7 @@ def __post_init__(self): self.key = parsed.path.lstrip("/") self._local_suffix = self._local_suffix_from_key(self.key) self._is_dir = None + self.logger = get_logger() def cleanup(self): # Close any open connections, unmount stuff, etc. @@ -288,8 +291,8 @@ async def inventory(self, cache: IOCacheStorageInterface): - cache.size """ if self.get_inventory_parent() in cache.exists_in_storage: - # bucket has been inventorized before, stop here - return + # bucket has been inventorized before, stop here + return # check if bucket exists if not self.bucket.exists(): @@ -381,29 +384,20 @@ def store_object(self): TODO: note from vsoch - I'm not sure I read this function name right, but I didn't find an equivalent "upload" function so I thought this might - be it. The original function comment is below. + be it. The original function comment is below. """ # Ensure that the object is stored at the location specified by # self.local_path(). try: - if not self.bucket.exists(): - self.client.create_bucket(self.bucket) + self.ensure_bucket_exists() # Distinguish between single file, and folder - f = self.local_path() - if os.path.isdir(f): - # Ensure the "directory" exists - self.blob.upload_from_string( - "", content_type="application/x-www-form-urlencoded;charset=UTF-8" - ) - for root, _, files in os.walk(f): - for filename in files: - filename = os.path.join(root, filename) - bucket_path = filename.lstrip(self.bucket.name).lstrip("/") - blob = self.bucket.blob(bucket_path) - blob.upload_from_filename(filename) + local_object = self.local_path() + if os.path.isdir(local_object): + self.upload_directory(local_directory_path=local_object) else: - self.blob.upload_from_filename(f) + self.blob.upload_from_filename(local_object) + except google.cloud.exceptions.Forbidden as e: raise WorkflowError( e, @@ -413,13 +407,57 @@ def store_object(self): "--scopes (see Snakemake documentation).", ) + def ensure_bucket_exists(self) -> None: + """ + Check that the bucket exists, if not create it. + """ + if not self.bucket.exists(): + self.client.create_bucket(self.bucket) + + def upload_directory(self, local_directory_path: Path): + """ + Upload a directory to the storage. + """ + self.ensure_bucket_exists() + + # if the local directory is empty, we need to create a blob + # with no content to represent the directory + if not os.listdir(local_directory_path): + self.blob.upload_from_string( + "", content_type="application/x-www-form-urlencoded;charset=UTF-8" + ) + + for root, _, files in os.walk(local_directory_path): + for filename in files: + relative_filepath = os.path.join(root, filename) + local_prefix = self.provider.local_prefix.as_posix() + + # remove the prefix ("".snakemake/storage/gcs/{bucket_name}/) + # this gives us the path to the file relative to the bucket + bucket_file_path = ( + relative_filepath.removeprefix(local_prefix) + .lstrip("/") + .removeprefix(self.bucket_name) + .lstrip("/") + ) + + blob = self.bucket.blob(bucket_file_path) + blob.upload_from_filename(relative_filepath) + @retry.Retry(predicate=google_cloud_retry_predicate) - def remove(self): + def remove(self) -> None: """ Remove the object from the storage. """ - # This was a total guess lol - self.blob.delete() + if self.is_directory(): + prefix = self.key + if not prefix.endswith("/"): + prefix += "/" + blobs = self.client.list_blobs(self.bucket_name, prefix=prefix) + for blob in blobs: + blob.delete() + else: + self.blob.delete() # The following to methods are only required if the class inherits from # StorageObjectGlob. diff --git a/tests/test_fake_gcs.py b/tests/test_fake_gcs.py index 63f70c1..45bf4cd 100644 --- a/tests/test_fake_gcs.py +++ b/tests/test_fake_gcs.py @@ -38,6 +38,7 @@ # Create a new Bucket bucket = client.bucket("snakemake-test-bucket") + try: client.create_bucket(bucket) except Conflict: @@ -54,6 +55,5 @@ blob = bucket.blob(file_name) blob.upload_from_string(contents) - assert not bucket.blob("foo").exists() print(list(bucket.list_blobs())) diff --git a/tests/tests.py b/tests/tests.py index 97349c5..f915d54 100644 --- a/tests/tests.py +++ b/tests/tests.py @@ -1,6 +1,5 @@ import os - -# from unittest.mock import MagicMock, patch +import shutil from typing import List, Optional, Type import uuid @@ -20,7 +19,7 @@ class TestStorage(TestStorageBase): __test__ = True - files_only = False + files_only = True # def get_query(self, tmp_path) -> str: return "gcs://snakemake-test-bucket/test-file.txt" @@ -41,35 +40,47 @@ def get_storage_provider_settings(self) -> Optional[StorageProviderSettingsBase] def get_example_args(self) -> List[str]: return [] - def test_storage_dbg(self, tmp_path): - assert not ( - self.store_only and self.retrieve_only - ), "store_only and retrieve_only may not be True at the same time" + # TODO remove if this is now in the base class + def test_storage_nonempty_directory(self, tmp_path): + # make a directory + tmpdir = "test_nonemptydir" - obj = self._get_obj(tmp_path, self.get_query(tmp_path)) + # store the directory + obj = self._get_obj(tmp_path, f"gcs://snakemake-test-bucket/{tmpdir}") stored = False try: if not self.retrieve_only: - obj.local_path().parent.mkdir(parents=True, exist_ok=True) - with open(obj.local_path(), "w") as f: + obj.local_path().mkdir(parents=True, exist_ok=True) + + assert obj.is_directory() + + print(obj.local_path()) + print("Writing a file in the directory") + # write a file in the directory + with open(obj.local_path() / "testfile.txt", "w") as f: f.write("test") f.flush() + + assert obj.bucket.exists() + assert obj.local_path().exists() and obj.local_path().is_dir() + print("Storing the directory") + obj.store_object() stored = True - obj.local_path().unlink() assert obj.exists() print(obj.mtime()) print(obj.size()) - if not self.store_only: - obj.local_path().parent.mkdir(parents=True, exist_ok=True) - obj.retrieve_object() + file = obj.local_path() / "testfile.txt" + assert file.exists() + print(file.read_text()) finally: if not self.retrieve_only and stored and self.delete: obj.remove() + shutil.rmtree(obj.local_path()) def test_list_candidate_matches(self, tmp_path): obj = self._get_obj(tmp_path, "gcs://snakemake-test-bucket/")