Merge branch 'master' into 201-experiment-with-upgrading-openapi-generator

Author: bisgaard-itis

clients/python/src/osparc/_api_files_api.py

@@ -5,7 +5,7 @@
 import logging
 import math
 from pathlib import Path
-from typing import Any, Iterator, List, Optional, Tuple, Union
+from typing import Any, Iterator, List, Optional, Tuple, Union, Final, Set
 from tempfile import NamedTemporaryFile
 
 import httpx
@@ -31,13 +31,16 @@
 import shutil
 from ._utils import (
     DEFAULT_TIMEOUT_SECONDS,
-    PaginationGenerator,
+    PaginationIterable,
     compute_sha256,
     file_chunk_generator,
+    Chunk,
 )
 
 _logger = logging.getLogger(__name__)
 
+_MAX_CONCURRENT_UPLOADS: Final[int] = 20
+
 
 class FilesApi(_FilesApi):
     _dev_features = [
@@ -116,16 +119,23 @@ def upload_file(
         self,
         file: Union[str, Path],
         timeout_seconds: int = DEFAULT_TIMEOUT_SECONDS,
+        max_concurrent_uploads: int = _MAX_CONCURRENT_UPLOADS,
         **kwargs,
     ):
         return asyncio.run(
-            self.upload_file_async(file=file, timeout_seconds=timeout_seconds, **kwargs)
+            self.upload_file_async(
+                file=file,
+                timeout_seconds=timeout_seconds,
+                max_concurrent_uploads=max_concurrent_uploads,
+                **kwargs,
+            )
         )
 
     async def upload_file_async(
         self,
         file: Union[str, Path],
         timeout_seconds: int = DEFAULT_TIMEOUT_SECONDS,
+        max_concurrent_uploads: int = _MAX_CONCURRENT_UPLOADS,
         **kwargs,
     ) -> File:
         if isinstance(file, str):
@@ -159,53 +169,66 @@ async def upload_file_async(
                 "Did not receive sufficient number of upload URLs from the server."
             )
 
-        uploaded_parts: list[UploadedPart] = []
+        abort_body = BodyAbortMultipartUploadV0FilesFileIdAbortPost(
+            client_file=client_file
+        )
+        upload_tasks: Set[asyncio.Task] = set()
+        uploaded_parts: List[UploadedPart] = []
+
         async with AsyncHttpClient(
-            configuration=self.api_client.configuration, timeout=timeout_seconds
-        ) as session:
-            with logging_redirect_tqdm():
-                _logger.debug("Uploading %s in %i chunk(s)", file.name, n_urls)
-                async for chunck, size in tqdm(
-                    file_chunk_generator(file, chunk_size),
-                    total=n_urls,
-                    disable=(not _logger.isEnabledFor(logging.DEBUG)),
-                ):
-                    index, url = next(url_iter)
-                    uploaded_parts.append(
-                        await self._upload_chunck(
-                            http_client=session,
-                            chunck=chunck,
-                            chunck_size=size,
-                            upload_link=url,
-                            index=index,
+            configuration=self.api_client.configuration,
+            method="post",
+            url=links.abort_upload,
+            body=abort_body.to_dict(),
+            base_url=self.api_client.configuration.host,
+            follow_redirects=True,
+            auth=self._auth,
+            timeout=timeout_seconds,
+        ) as api_server_session:
+            async with AsyncHttpClient(
+                configuration=self.api_client.configuration, timeout=timeout_seconds
+            ) as s3_session:
+                with logging_redirect_tqdm():
+                    _logger.debug("Uploading %s in %i chunk(s)", file.name, n_urls)
+                    async for chunk in tqdm(
+                        file_chunk_generator(file, chunk_size),
+                        total=n_urls,
+                        disable=(not _logger.isEnabledFor(logging.DEBUG)),
+                    ):  # type: ignore
+                        assert isinstance(chunk, Chunk)  # nosec
+                        index, url = next(url_iter)
+                        upload_tasks.add(
+                            asyncio.create_task(
+                                self._upload_chunck(
+                                    http_client=s3_session,
+                                    chunck=chunk.data,
+                                    chunck_size=chunk.nbytes,
+                                    upload_link=url,
+                                    index=index,
+                                )
+                            )
                         )
-                    )
+                        while (len(upload_tasks) >= max_concurrent_uploads) or (
+                            chunk.is_last_chunk and len(upload_tasks) > 0
+                        ):
+                            done, upload_tasks = await asyncio.wait(
+                                upload_tasks, return_when=asyncio.FIRST_COMPLETED
+                            )
+                            for task in done:
+                                uploaded_parts.append(task.result())
 
-            abort_body = BodyAbortMultipartUploadV0FilesFileIdAbortPost(
-                client_file=client_file
+            _logger.debug(
+                ("Completing upload of %s " "(this might take a couple of minutes)..."),
+                file.name,
             )
-            async with AsyncHttpClient(
-                configuration=self.api_client.configuration,
-                method="post",
-                url=links.abort_upload,
-                body=abort_body.to_dict(),
-                base_url=self.api_client.configuration.host,
-                follow_redirects=True,
-                auth=self._auth,
-                timeout=timeout_seconds,
-            ) as session:
-                _logger.debug(
-                    (
-                        "Completing upload of %s "
-                        "(this might take a couple of minutes)..."
-                    ),
-                    file.name,
-                )
-                server_file: File = await self._complete_multipart_upload(
-                    session, links.complete_upload, client_file, uploaded_parts
-                )
-                _logger.debug("File upload complete: %s", file.name)
-                return server_file
+            server_file: File = await self._complete_multipart_upload(
+                api_server_session,
+                links.complete_upload,  # type: ignore
+                client_file,
+                uploaded_parts,
+            )
+            _logger.debug("File upload complete: %s", file.name)
+            return server_file
 
     async def _complete_multipart_upload(
         self,
@@ -250,15 +273,19 @@ def _search_files(
         file_id: Optional[str] = None,
         sha256_checksum: Optional[str] = None,
         timeout_seconds: int = DEFAULT_TIMEOUT_SECONDS,
-    ) -> PaginationGenerator:
+    ) -> PaginationIterable:
+        kwargs = {
+            "file_id": file_id,
+            "sha256_checksum": sha256_checksum,
+            "_request_timeout": timeout_seconds,
+        }
+
         def _pagination_method():
             return super(FilesApi, self).search_files_page(
-                file_id=file_id,
-                sha256_checksum=sha256_checksum,
-                _request_timeout=timeout_seconds,
+                **{k: v for k, v in kwargs.items() if v is not None}
             )
 
-        return PaginationGenerator(
+        return PaginationIterable(
             first_page_callback=_pagination_method,
             api_client=self.api_client,
             base_url=self.api_client.configuration.host,

clients/python/src/osparc/_api_solvers_api.py

@@ -21,7 +21,7 @@
 from ._utils import (
     _DEFAULT_PAGINATION_LIMIT,
     _DEFAULT_PAGINATION_OFFSET,
-    PaginationGenerator,
+    PaginationIterable,
 )
 import warnings
 from tempfile import NamedTemporaryFile
@@ -60,7 +60,7 @@ def list_solver_ports(
         )
         return page.items if page.items else []
 
-    def iter_jobs(self, solver_key: str, version: str, **kwargs) -> PaginationGenerator:
+    def iter_jobs(self, solver_key: str, version: str, **kwargs) -> PaginationIterable:
         """Returns an iterator through which one can iterate over
         all Jobs submitted to the solver
 
@@ -85,14 +85,14 @@ def _pagination_method():
                 **kwargs,
             )
 
-        return PaginationGenerator(
+        return PaginationIterable(
             first_page_callback=_pagination_method,
             api_client=self.api_client,
             base_url=self.api_client.configuration.host,
             auth=self._auth,
         )
 
-    def jobs(self, solver_key: str, version: str, **kwargs) -> PaginationGenerator:
+    def jobs(self, solver_key: str, version: str, **kwargs) -> PaginationIterable:
         warnings.warn(
             "The 'jobs' method is deprecated and will be removed in a future version. "
             "Please use 'iter_jobs' instead.",

clients/python/src/osparc/_api_studies_api.py

@@ -28,7 +28,7 @@
 from ._utils import (
     _DEFAULT_PAGINATION_LIMIT,
     _DEFAULT_PAGINATION_OFFSET,
-    PaginationGenerator,
+    PaginationIterable,
 )
 import warnings
 
@@ -86,7 +86,7 @@ def clone_study(self, study_id: str, **kwargs):
         kwargs = {**kwargs, **ParentProjectInfo().model_dump(exclude_none=True)}
         return super().clone_study(study_id, **kwargs)
 
-    def iter_studies(self, **kwargs) -> PaginationGenerator:
+    def iter_studies(self, **kwargs) -> PaginationIterable:
         def _pagination_method():
             page_study = self.list_studies(
                 limit=_DEFAULT_PAGINATION_LIMIT,
@@ -96,14 +96,14 @@ def _pagination_method():
             assert isinstance(page_study, PageStudy)  # nosec
             return page_study
 
-        return PaginationGenerator(
+        return PaginationIterable(
             first_page_callback=_pagination_method,
             api_client=self.api_client,
             base_url=self.api_client.configuration.host,
             auth=self._auth,
         )
 
-    def studies(self, **kwargs) -> PaginationGenerator:
+    def studies(self, **kwargs) -> PaginationIterable:
         warnings.warn(
             "The 'studies' method is deprecated and will be removed in a future version. "
             "Please use 'iter_studies' instead.",

clients/python/src/osparc/_utils.py

@@ -1,8 +1,16 @@
 import asyncio
 import hashlib
 from pathlib import Path
-from typing import AsyncGenerator, Callable, Generator, Optional, Tuple, TypeVar, Union
-
+from typing import (
+    AsyncGenerator,
+    Callable,
+    Optional,
+    TypeVar,
+    Union,
+    NamedTuple,
+    Generator,
+)
+from collections.abc import Iterable, Sized
 import httpx
 from osparc_client import (
     ApiClient,
@@ -15,7 +23,7 @@
     Study,
 )
 import aiofiles
-from ._exceptions import RequestError
+from .exceptions import RequestError
 
 _KB = 1024  # in bytes
 _MB = _KB * 1024  # in bytes
@@ -30,8 +38,11 @@
 T = TypeVar("T", Job, File, Solver, Study)
 
 
-class PaginationGenerator:
-    """Class for wrapping paginated http methods as generators"""
+class PaginationIterable(Iterable, Sized):
+    """Class for wrapping paginated http methods as iterables. It supports three simple operations:
+    - for elm in pagination_iterable
+    - elm = next(pagination_iterable)
+    - len(pagination_iterable)"""
 
     def __init__(
         self,
@@ -75,9 +86,15 @@ def __iter__(self) -> Generator[T, None, None]:
             page = self._api_client._ApiClient__deserialize(response.json(), type(page))
 
 
+class Chunk(NamedTuple):
+    data: bytes
+    nbytes: int
+    is_last_chunk: bool
+
+
 async def file_chunk_generator(
     file: Path, chunk_size: int
-) -> AsyncGenerator[Tuple[bytes, int], None]:
+) -> AsyncGenerator[Chunk, None]:
     if not file.is_file():
         raise RuntimeError(f"{file} must be a file")
     if chunk_size <= 0:
@@ -94,8 +111,10 @@ async def file_chunk_generator(
             )
             assert nbytes > 0
             chunk = await f.read(nbytes)
-            yield chunk, nbytes
             bytes_read += nbytes
+            yield Chunk(
+                data=chunk, nbytes=nbytes, is_last_chunk=(bytes_read == file_size)
+            )
 
 
 S = TypeVar("S")

clients/python/test/e2e/conftest.py

@@ -18,6 +18,7 @@
 from packaging.version import Version
 from pydantic import ByteSize
 from typing import NamedTuple, Final
+from memory_profiler import memory_usage
 
 try:
     from osparc._settings import ConfigurationEnvVars
@@ -29,6 +30,8 @@
 _MB: ByteSize = ByteSize(_KB * 1024)  # in bytes
 _GB: ByteSize = ByteSize(_MB * 1024)  # in bytes
 
+_logger = logging.getLogger(__name__)
+
 # Dictionary to store start times of tests
 _test_start_times = {}
 
@@ -140,6 +143,7 @@ def async_client() -> Iterable[AsyncClient]:
 class ServerFile(NamedTuple):
     server_file: osparc.File
     local_file: Path
+    upload_ram_usage: int
 
 
 @pytest.fixture(scope="session")
@@ -160,11 +164,23 @@ def large_server_file(
     assert (
         tmp_file.stat().st_size == _file_size
     ), f"Could not create file of size: {_file_size}"
-    uploaded_file: osparc.File = files_api.upload_file(tmp_file)
+    ram_statistics, uploaded_file = memory_usage(
+        (files_api.upload_file, (tmp_file,)), retval=True
+    )
 
-    yield ServerFile(local_file=tmp_file, server_file=uploaded_file)
+    yield ServerFile(
+        local_file=tmp_file,
+        server_file=uploaded_file,
+        upload_ram_usage=max(ram_statistics) - min(ram_statistics),
+    )
 
-    files_api.delete_file(uploaded_file.id)
+    try:
+        files_api.delete_file(uploaded_file.id)
+    except osparc.ApiException:
+        _logger.warning(
+            f"Could not delete file on server in {file_with_number.__name__}",
+            exc_info=True,
+        )
 
 
 @pytest.fixture
@@ -198,4 +214,10 @@ def file_with_number(
     server_file = files_api.upload_file(file)
     yield server_file
 
-    files_api.delete_file(server_file.id)
+    try:
+        files_api.delete_file(server_file.id)
+    except osparc.ApiException:
+        _logger.warning(
+            f"Could not delete file on server in {file_with_number.__name__}",
+            exc_info=True,
+        )