pybiolib 1.1.1881__py3-none-any.whl → 1.1.2193__py3-none-any.whl

{pybiolib-1.1.1881.dist-info → pybiolib-1.1.2193.dist-info}/RECORD

@@ -1,51 +1,66 @@
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 biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFveE,715
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+biolib/typing_utils.py,sha256=ntzrlyTkUaO2OtccLYzCAGztGdca0WT5fikJUmSkT-Y,148
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
-biolib/user/sign_in.py,sha256=q-E2B3wLVwPU5plbITJXP4GDWWUzUcDpYu_y8BShNQ8,2039
+biolib/user/sign_in.py,sha256=XTAmRPKfmg7VAaB8cT5wcmfxoPXeHqY8LmDiADF7zbw,2064
 biolib/utils/__init__.py,sha256=fwjciJyJicvYyZcVTzfDBgD0SKY13DeXqvTeG4qZIy8,5548
 biolib/utils/app_uri.py,sha256=Yq_-_VGugQhMMo6mM5f0G9yNlLkr0WK4j0Nrf3FE4xQ,2171
 biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3100
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
-biolib/utils/seq_util.py,sha256=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
+biolib/utils/seq_util.py,sha256=ZQFcaE37B2dtucN2zDjOmdya_X0ITc1zBFZJNQY13XA,5183
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.1881.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1881.dist-info/METADATA,sha256=oanwAPIfyI5nATML26HjNK4sjPb2ciuoyP2jLxg8Kbs,1508
-pybiolib-1.1.1881.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1881.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1881.dist-info/RECORD,,
+pybiolib-1.1.2193.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2193.dist-info/METADATA,sha256=NCFsHsCnbnOhw1O2L-polZfFa2pNdtA89TfBW7f_o7E,1508
+pybiolib-1.1.2193.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2193.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2193.dist-info/RECORD,,

biolib/experiments/types.py

@@ -1,9 +0,0 @@
-from biolib.typing_utils import TypedDict
-
-
-class ExperimentDict(TypedDict):
-    created_at: str
-    job_count: int
-    job_running_count: int
-    name: str
-    uuid: str

biolib/lfs/__init__.py

@@ -1,4 +0,0 @@
-from .cache import prune_lfs_cache
-from .utils import \
-    push_large_file_system, \
-    create_large_file_system

biolib/lfs/utils.py

@@ -1,153 +0,0 @@
-import io
-import os
-import zipfile as zf
-from pathlib import Path
-
-from biolib import utils, api
-from biolib.biolib_api_client import BiolibApiClient
-from biolib.biolib_api_client.lfs_types import LargeFileSystem, LargeFileSystemVersion
-from biolib.biolib_logging import logger
-from biolib.biolib_errors import BioLibError
-from biolib.typing_utils import List, Tuple, Iterator, Optional
-from biolib.utils.app_uri import parse_app_uri
-
-
-def get_files_and_size_of_directory(directory: str) -> Tuple[List[str], int]:
-    data_size = 0
-    file_list: List[str] = []
-
-    for path, _, files in os.walk(directory):
-        for file in files:
-            file_path = os.path.join(path, file)
-            if os.path.islink(file_path):
-                continue  # skip symlinks
-
-            relative_file_path = file_path[len(directory) + 1:]  # +1 to remove starting slash
-            file_list.append(relative_file_path)
-            data_size += os.path.getsize(file_path)
-
-    return file_list, data_size
-
-
-def get_iterable_zip_stream(files: List[str], chunk_size: int) -> Iterator[bytes]:
-    class ChunkedIOBuffer(io.RawIOBase):
-        def __init__(self, chunk_size: int):
-            super().__init__()
-            self.chunk_size = chunk_size
-            self.tmp_data = bytearray()
-
-        def get_buffer_size(self):
-            return len(self.tmp_data)
-
-        def read_chunk(self):
-            chunk = bytes(self.tmp_data[:self.chunk_size])
-            self.tmp_data = self.tmp_data[self.chunk_size:]
-            return chunk
-
-        def write(self, data):
-            data_length = len(data)
-            self.tmp_data += data
-            return data_length
-
-    # create chunked buffer to hold data temporarily
-    io_buffer = ChunkedIOBuffer(chunk_size)
-
-    # create zip writer that will write to the io buffer
-    zip_writer = zf.ZipFile(io_buffer, mode='w')  # type: ignore
-
-    for file_path in files:
-        # generate zip info and prepare zip pointer for writing
-        z_info = zf.ZipInfo.from_file(file_path)
-        zip_pointer = zip_writer.open(z_info, mode='w')
-        if Path(file_path).is_file():
-            # read file chunk by chunk
-            with open(file_path, 'br') as file_pointer:
-                while True:
-                    chunk = file_pointer.read(chunk_size)
-                    if len(chunk) == 0:
-                        break
-                    # write the chunk to the zip
-                    zip_pointer.write(chunk)
-                    # if writing the chunk caused us to go over chunk_size, flush it
-                    if io_buffer.get_buffer_size() > chunk_size:
-                        yield io_buffer.read_chunk()
-
-        zip_pointer.close()
-
-    # flush any remaining data in the stream (e.g. zip file meta data)
-    zip_writer.close()
-    while True:
-        chunk = io_buffer.read_chunk()
-        if len(chunk) == 0:
-            break
-        yield chunk
-
-
-def create_large_file_system(lfs_uri: str) -> str:
-    BiolibApiClient.assert_is_signed_in(authenticated_action_description='create a Large File System')
-
-    uri_parsed = parse_app_uri(lfs_uri)
-    response = api.client.post(
-        path='/lfs/',
-        data={
-            'account_handle': uri_parsed['account_handle_normalized'],
-            'name': uri_parsed['app_name'],
-        },
-    )
-    lfs: LargeFileSystem = response.json()
-    logger.info(f"Successfully created new Large File System '{lfs['uri']}'")
-    return lfs['uri']
-
-
-def push_large_file_system(lfs_uri: str, input_dir: str, chunk_size_in_mb: Optional[int] = None) -> str:
-    BiolibApiClient.assert_is_signed_in(authenticated_action_description='push data to a Large File System')
-
-    if not os.path.isdir(input_dir):
-        raise BioLibError(f'Could not find folder at {input_dir}')
-
-    if os.path.realpath(input_dir) == '/':
-        raise BioLibError('Pushing your root directory is not possible')
-
-    original_working_dir = os.getcwd()
-    os.chdir(input_dir)
-    files_to_zip, data_size_in_bytes = get_files_and_size_of_directory(directory=os.getcwd())
-
-    if data_size_in_bytes > 4_500_000_000_000:
-        raise BioLibError('Attempted to push directory with a size larger than the limit of 4.5 TB')
-
-    min_chunk_size_bytes = 10_000_000
-    chunk_size_in_bytes: int
-    if chunk_size_in_mb:
-        chunk_size_in_bytes = chunk_size_in_mb * 1_000_000  # Convert megabytes to bytes
-        if chunk_size_in_bytes < min_chunk_size_bytes:
-            logger.warning('Specified chunk size is too small, using minimum of 10 MB instead.')
-            chunk_size_in_bytes = min_chunk_size_bytes
-    else:
-        # Calculate chunk size based on max chunk count of 10_000, using 9_000 to be on the safe side
-        chunk_size_in_bytes = max(min_chunk_size_bytes, int(data_size_in_bytes / 9_000))
-
-    data_size_in_mb = round(data_size_in_bytes / 10 ** 6)
-    print(f'Zipping {len(files_to_zip)} files, in total ~{data_size_in_mb}mb of data')
-
-    response = api.client.post(path='/lfs/versions/', data={'resource_uri': lfs_uri})
-    lfs_version: LargeFileSystemVersion = response.json()
-    iterable_zip_stream = get_iterable_zip_stream(files=files_to_zip, chunk_size=chunk_size_in_bytes)
-
-    multipart_uploader = utils.MultiPartUploader(
-        use_process_pool=True,
-        get_presigned_upload_url_request=dict(
-            headers=None,
-            requires_biolib_auth=True,
-            path=f"/lfs/versions/{lfs_version['uuid']}/presigned_upload_url/",
-        ),
-        complete_upload_request=dict(
-            headers=None,
-            requires_biolib_auth=True,
-            path=f"/lfs/versions/{lfs_version['uuid']}/complete_upload/",
-        ),
-    )
-
-    multipart_uploader.upload(payload_iterator=iterable_zip_stream, payload_size_in_bytes=data_size_in_bytes)
-    os.chdir(original_working_dir)
-    logger.info(f"Successfully pushed a new LFS version '{lfs_version['uri']}'")
-    return lfs_version['uri']