diff --git a/mypy.ini b/mypy.ini --- a/mypy.ini +++ b/mypy.ini @@ -22,3 +22,6 @@ [mypy-pytest.*] ignore_missing_imports = True + +[mypy-tqdm.*] +ignore_missing_imports = True diff --git a/requirements-luigi.txt b/requirements-luigi.txt --- a/requirements-luigi.txt +++ b/requirements-luigi.txt @@ -1 +1,2 @@ luigi +tqdm diff --git a/requirements-swh-luigi.txt b/requirements-swh-luigi.txt --- a/requirements-swh-luigi.txt +++ b/requirements-swh-luigi.txt @@ -1 +1 @@ -swh.dataset[luigi] >= v0.3.2 +swh.dataset[luigi] >= v1.0.1 diff --git a/swh/graph/luigi.py b/swh/graph/luigi.py --- a/swh/graph/luigi.py +++ b/swh/graph/luigi.py @@ -56,6 +56,19 @@ When the compression pipeline is run in separate steps, each of the steps is recorded as an object in the root list. + +S3 layout +--------- + +As ``.bin`` files are meant to be accessed randomly, they are uncompressed on disk. +However, this is undesirable on at-rest/long-term storage like on S3, because +some are very sparse (eg. :file:`graph.property.committer_timestamp.bin` can be +quickly compressed from 300 to 1GB). + +Therefore, these files are compressed to ``.bin.zst``, and need to be decompressed +when downloading. + +The layout is otherwise the same as the file layout. """ # WARNING: do not import unnecessary things here to keep cli startup time under @@ -64,11 +77,11 @@ import luigi -from swh.dataset.luigi import Format, LocalExport, ObjectType +from swh.dataset.luigi import Format, LocalExport, ObjectType, S3PathParameter class CompressGraph(luigi.Task): - local_export_path = luigi.PathParameter() + local_export_path = luigi.PathParameter(significant=False) local_graph_path = luigi.PathParameter() batch_size = luigi.IntParameter( default=0, @@ -184,3 +197,240 @@ ) with self._compression_meta().open("w") as fd: json.dump(meta, fd, indent=4) + + +class UploadGraphToS3(luigi.Task): + """Uploads a local compressed graphto S3; creating automatically if it does + not exist. + + Example invocation:: + + luigi --local-scheduler --module swh.graph.luigi UploadGraphToS3 \ + --local-graph-path=graph/ \ + --s3-graph-path=s3://softwareheritage/graph/swh_2022-11-08/compressed/ + """ + + local_graph_path = luigi.PathParameter(significant=False) + s3_graph_path = S3PathParameter() + + def requires(self) -> List[luigi.Task]: + """Returns a :class:`CompressGraph` task that writes local files at the + expected location.""" + return [ + CompressGraph( + local_graph_path=self.local_graph_path, + ) + ] + + def output(self) -> List[luigi.Target]: + """Returns stamp and meta paths on S3.""" + return [self._meta()] + + def _meta(self): + import luigi.contrib.s3 + + return luigi.contrib.s3.S3Target(f"{self.s3_graph_path}/meta/compression.json") + + def run(self) -> None: + """Copies all files: first the graph itself, then :file:`meta/compression.json`.""" + import subprocess + import tempfile + + import luigi.contrib.s3 + import tqdm + + compression_metadata_path = self.local_graph_path / "meta" / "compression.json" + seen_compression_metadata = False + + client = luigi.contrib.s3.S3Client() + + # recursively copy local files to S3, and end with compression metadata + paths = list(self.local_graph_path.glob("**/*")) + for (i, path) in tqdm.tqdm( + list(enumerate(paths)), + desc="Uploading compressed graph", + ): + if path == compression_metadata_path: + # Write it last + seen_compression_metadata = True + continue + if path.is_dir(): + continue + relative_path = path.relative_to(self.local_graph_path) + self.set_progress_percentage(int(i * 100 / len(paths))) + + if path.suffix == ".bin": + # Large sparse file; store it compressed on S3. + with tempfile.NamedTemporaryFile( + prefix=path.stem, suffix=".bin.zst" + ) as fd: + self.set_status_message(f"Compressing {relative_path}") + subprocess.run( + ["zstdmt", "--force", "--keep", path, "-o", fd.name], check=True + ) + self.set_status_message(f"Uploading {relative_path} (compressed)") + client.put_multipart( + fd.name, + f"{self.s3_graph_path}/{relative_path}.zst", + ACL="public-read", + ) + else: + self.set_status_message(f"Uploading {relative_path}") + client.put_multipart( + path, f"{self.s3_graph_path}/{relative_path}", ACL="public-read" + ) + + assert ( + seen_compression_metadata + ), "did not see meta/compression.json in directory listing" + + # Write it last, to act as a stamp + client.put( + compression_metadata_path, + self._meta().path, + ACL="public-read", + ) + + +class DownloadGraphFromS3(luigi.Task): + """Downloads a local dataset graph from S3. + + This performs the inverse operation of :class:`UploadGraphToS3` + + Example invocation:: + + luigi --local-scheduler --module swh.graph.luigi DownloadGraphFromS3 \ + --local-graph-path=graph/ \ + --s3-graph-path=s3://softwareheritage/graph/swh_2022-11-08/compressed/ + """ + + local_graph_path = luigi.PathParameter() + s3_graph_path = S3PathParameter(significant=False) + + def requires(self) -> List[luigi.Task]: + """Returns a :class:`ExportGraph` task that writes local files at the + expected location.""" + return [ + UploadGraphToS3( + local_graph_path=self.local_graph_path, + s3_graph_path=self.s3_graph_path, + ) + ] + + def output(self) -> List[luigi.Target]: + """Returns stamp and meta paths on the local filesystem.""" + return [self._meta()] + + def _meta(self): + return luigi.LocalTarget(self.local_graph_path / "meta" / "export.json") + + def run(self) -> None: + """Copies all files: first the graph itself, then :file:`meta/compression.json`.""" + import subprocess + import tempfile + + import luigi.contrib.s3 + import tqdm + + client = luigi.contrib.s3.S3Client() + + compression_metadata_path = f"{self.s3_graph_path}/meta/compression.json" + seen_compression_metadata = False + + # recursively copy local files to S3, and end with compression metadata + files = list(client.list(self.s3_graph_path)) + for (i, file_) in tqdm.tqdm( + list(enumerate(files)), + desc="Downloading", + ): + if file_ == compression_metadata_path: + # Will copy it last + seen_compression_metadata = True + continue + self.set_progress_percentage(int(i * 100 / len(files))) + local_path = self.local_graph_path / file_ + local_path.parent.mkdir(parents=True, exist_ok=True) + if file_.endswith(".bin.zst"): + # The file was compressed before uploading to S3, we need it + # to be decompressed locally + with tempfile.NamedTemporaryFile( + prefix=local_path.stem, suffix=".bin.zst" + ) as fd: + self.set_status_message(f"Downloading {file_} (compressed)") + client.get( + f"{self.s3_graph_path}/{file_}", + fd.name, + ) + self.set_status_message(f"Decompressing {file_}") + subprocess.run( + [ + "zstdmt", + "--force", + "-d", + fd.name, + "-o", + str(local_path)[0:-4], + ], + check=True, + ) + else: + self.set_status_message(f"Downloading {file_}") + client.get( + f"{self.s3_graph_path}/{file_}", + str(local_path), + ) + + assert ( + seen_compression_metadata + ), "did not see meta/compression.json in directory listing" + + # Write it last, to act as a stamp + client.get( + compression_metadata_path, + self._meta().path, + ) + + +class LocalGraph(luigi.Task): + """Task that depends on a local dataset being present -- either directly from + :class:`ExportGraph` or via :class:`DownloadGraphFromS3`. + """ + + local_graph_path = luigi.PathParameter() + compression_task_type = luigi.TaskParameter( + default=DownloadGraphFromS3, + significant=False, + description="""The task used to get the compressed graph if it is not present. + Should be either ``swh.graph.luigi.CompressGraph`` or + ``swh.graph.luigi.DownloadGraphFromS3``.""", + ) + + def requires(self) -> List[luigi.Task]: + """Returns an instance of either :class:`CompressGraph` or + :class:`DownloadGraphFromS3` depending on the value of + :attr:`compression_task_type`.""" + + if issubclass(self.compression_task_type, CompressGraph): + return [ + CompressGraph( + local_graph_path=self.local_graph_path, + ) + ] + elif issubclass(self.compression_task_type, DownloadGraphFromS3): + return [ + DownloadGraphFromS3( + local_graph_path=self.local_graph_path, + ) + ] + else: + raise ValueError( + f"Unexpected compression_task_type: " + f"{self.compression_task_type.__name__}" + ) + + def output(self) -> List[luigi.Target]: + """Returns stamp and meta paths on the local filesystem.""" + return [self._meta()] + + def _meta(self): + return luigi.LocalTarget(self.local_graph_path / "meta" / "compression.json")