pybiolib 1.1.2090__py3-none-any.whl → 1.1.2109__py3-none-any.whl

biolib/cli/data_record.py

@@ -1,11 +1,12 @@
+import json
 import logging
 import os
+from typing import Dict, List
 
 import click
 
 from biolib._data_record.data_record import DataRecord
 from biolib.biolib_logging import logger, logger_no_user_data
-from biolib.sdk import create_data_record
 from biolib.typing_utils import Optional
 
 
@@ -16,11 +17,18 @@ def data_record() -> None:
 
 
 @data_record.command(help='Create a Data Record')
-@click.option('--destination', type=str, required=True)
+@click.argument('uri', required=True)
+@click.option('--data-path', required=True, type=click.Path(exists=True))
+def create(uri: str, data_path: str) -> None:
+    DataRecord.create(destination=uri, data_path=data_path)
+
+
+@data_record.command(help='Update a Data Record')
+@click.argument('uri', required=True)
 @click.option('--data-path', required=True, type=click.Path(exists=True))
-@click.option('--name', type=str, required=False)
-def create(destination: str, data_path: str, name: Optional[str] = None) -> None:
-    create_data_record(destination=destination, data_path=data_path, name=name)
+@click.option('--chunk-size', default=None, required=False, type=click.INT, help='The size of each chunk (In MB)')
+def update(uri: str, data_path: str, chunk_size: Optional[int]) -> None:
+    DataRecord.get_by_uri(uri=uri).update(data_path=data_path, chunk_size_in_mb=chunk_size)
 
 
 @data_record.command(help='Download files from a Data Record')
@@ -42,3 +50,30 @@ def download(uri: str, file: Optional[str], path_filter: Optional[str]) -> None:
     else:
         assert not os.path.exists(record.name), f'Directory with name {record.name} already exists in current directory'
         record.save_files(output_dir=record.name, path_filter=path_filter)
+
+
+@data_record.command(help='Describe a Data Record')
+@click.argument('uri', required=True)
+@click.option('--json', 'output_as_json', is_flag=True, default=False, required=False, help='Format output as JSON')
+def describe(uri: str, output_as_json: bool) -> None:
+    record = DataRecord.get_by_uri(uri)
+    files_info: List[Dict] = []
+    total_size_in_bytes = 0
+    for file in record.list_files():
+        files_info.append({'path': file.path, 'size_bytes': file.length})
+        total_size_in_bytes += file.length
+
+    if output_as_json:
+        print(
+            json.dumps(
+                obj={'uri': record.uri, 'size_bytes': total_size_in_bytes, 'files': files_info},
+                indent=4,
+            )
+        )
+    else:
+        print(f'Data Record {record.uri}\ntotal {total_size_in_bytes} bytes\n')
+        print('size bytes    path')
+        for file_info in files_info:
+            size_string = str(file_info['size_bytes'])
+            leading_space_string = ' ' * (10 - len(size_string))
+            print(f"{leading_space_string}{size_string}    {file_info['path']}")

biolib/cli/lfs.py

@@ -21,6 +21,7 @@ def lfs() -> None:
 @lfs.command(help='Create a Large File System')
 @click.argument('uri', required=True)
 def create(uri: str) -> None:
+    logger.warning('This is command deprecated, please use "biolib data-record create" instead.')
     logger.configure(default_log_level=logging.INFO)
     logger_no_user_data.configure(default_log_level=logging.INFO)
     DataRecord.create(destination=uri)
@@ -31,6 +32,7 @@ def create(uri: str) -> None:
 @click.option('--path', required=True, type=click.Path(exists=True))
 @click.option('--chunk-size', default=None, required=False, type=click.INT, help='The size of each chunk (In MB)')
 def push(uri: str, path: str, chunk_size: Optional[int]) -> None:
+    logger.warning('This is command deprecated, please use "biolib data-record update" instead.')
     logger.configure(default_log_level=logging.INFO)
     logger_no_user_data.configure(default_log_level=logging.INFO)
     try:
@@ -44,6 +46,7 @@ def push(uri: str, path: str, chunk_size: Optional[int]) -> None:
 @click.argument('uri', required=True)
 @click.option('--file-path', required=True, type=str)
 def download_file(uri: str, file_path: str) -> None:
+    logger.warning('This is command deprecated, please use "biolib data-record download" instead.')
     logger.configure(default_log_level=logging.INFO)
     logger_no_user_data.configure(default_log_level=logging.INFO)
     try:
@@ -66,6 +69,7 @@ def download_file(uri: str, file_path: str) -> None:
 @click.argument('uri', required=True)
 @click.option('--json', 'output_as_json', is_flag=True, default=False, required=False, help='Format output as JSON')
 def describe(uri: str, output_as_json: bool) -> None:
+    logger.warning('This is command deprecated, please use "biolib data-record describe" instead.')
     data_record = DataRecord.get_by_uri(uri)
     files_info: List[Dict] = []
     total_size_in_bytes = 0

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -270,6 +270,8 @@ class DockerExecutor:
     # TODO: type this method
     def _initialize_docker_container(self, module_input):
         try:
+            job_uuid = self._options['job']['public_id']
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container...')
             module = self._options['module']
             logger.debug(f"Initializing docker container with command: {module['command']}")
 
@@ -314,6 +316,7 @@ class DockerExecutor:
                     }
                 )
 
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Getting IPs for proxies...')
             for proxy in self._options['remote_host_proxies']:
                 proxy_ip = proxy.get_ip_address_on_network(internal_network)
                 if proxy.is_app_caller_proxy:
@@ -332,6 +335,7 @@ class DockerExecutor:
                 else:
                     extra_hosts[proxy.hostname] = proxy_ip
 
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Constructing container args...')
             create_container_args = {
                 'environment': environment_vars,
                 'extra_hosts': extra_hosts,
@@ -368,9 +372,10 @@ class DockerExecutor:
             if docker_runtime is not None:
                 create_container_args['runtime'] = docker_runtime
 
-            self._docker_container = BiolibDockerClient.get_docker_client().containers.create(**create_container_args)
-
-            logger_no_user_data.debug('Finished initializing docker container')
+            docker_client = BiolibDockerClient.get_docker_client()
+            logger_no_user_data.debug(f'Job "{job_uuid}" initializing Docker container. Creating container...')
+            self._docker_container = docker_client.containers.create(**create_container_args)
+            logger_no_user_data.debug(f'Job "{job_uuid}" finished initializing Docker container.')
         except Exception as exception:
             raise ComputeProcessException(
                 exception, SystemExceptionCodes.FAILED_TO_START_COMPUTE_CONTAINER.value, self._send_system_exception

{pybiolib-1.1.2090.dist-info → pybiolib-1.1.2109.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.2090
+Version: 1.1.2109
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.2090.dist-info → pybiolib-1.1.2109.dist-info}/RECORD

@@ -51,10 +51,10 @@ biolib/biolib_errors.py,sha256=5m4lK2l39DafpoXBImEBD4EPH3ayXBX0JgtPzmGClow,689
 biolib/biolib_logging.py,sha256=J3E5H_LL5k6ZUim2C8gqN7E6lCBZMTpO4tnMpOPwG9U,2854
 biolib/cli/__init__.py,sha256=0v3c_J-U0k46c5ZWeQjLG_kTaKDJm81LBxQpDO2B_aI,1286
 biolib/cli/auth.py,sha256=rpWGmXs6Fz6CGrO9K8ibPRszOdXG78Vig_boKaVCD9A,2082
-biolib/cli/data_record.py,sha256=ZlP1o7lKqL-ebmL2d-_L8Pmdd2DmS2Imk_a1C8AGLc4,1809
+biolib/cli/data_record.py,sha256=oDy8U6mv-h-hbeMihXRzVEvM-WrGQq6oBiBl3xDRaXs,3220
 biolib/cli/download_container.py,sha256=HIZVHOPmslGE5M2Dsp9r2cCkAEJx__vcsDz5Wt5LRos,483
 biolib/cli/init.py,sha256=wQOfii_au-d30Hp7DdH-WVw-WVraKvA_zY4za1w7DE8,821
-biolib/cli/lfs.py,sha256=j9hERvjh1QLhn_KbomLkPWIOPa1MYOajUpoo9r6EmVc,3755
+biolib/cli/lfs.py,sha256=z2qHUwink85mv9yDgifbVKkVwuyknGhMDTfly_gLKJM,4151
 biolib/cli/push.py,sha256=TFi7O9tJ3zFe0VmtVTV3Vh9_xIMHnrc41xxcaBKU46g,813
 biolib/cli/run.py,sha256=BbvXLQ-XibjQ71Y2d4URMH_8dflNVwM0i3TIWhw_u_c,1634
 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
@@ -68,7 +68,7 @@ biolib/compute_node/job_worker/cache_state.py,sha256=MwjSRzcJJ_4jybqvBL4xdgnDYSI
 biolib/compute_node/job_worker/cache_types.py,sha256=ajpLy8i09QeQS9dEqTn3T6NVNMY_YsHQkSD5nvIHccQ,818
 biolib/compute_node/job_worker/docker_image_cache.py,sha256=ansHIkJIq_EMW1nZNlW-RRLVVeKWTbzNICYaOHpKiRE,7460
 biolib/compute_node/job_worker/executors/__init__.py,sha256=bW6t1qi3PZTlHM4quaTLa8EI4ALTCk83cqcVJfJfJfE,145
-biolib/compute_node/job_worker/executors/docker_executor.py,sha256=81ltJvSDpCPBgbffnSQF-fiRpk_94sWZWJRcP0IW_5k,27393
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=2H7GooL0oAifPcbie0unatB4fRoHyqbsr6S91uagc_g,27952
 biolib/compute_node/job_worker/executors/docker_types.py,sha256=VhsU1DKtJjx_BbCkVmiPZPH4ROiL1ygW1Y_s1Kbpa2o,216
 biolib/compute_node/job_worker/executors/tars/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/job_worker/executors/types.py,sha256=yP5gG39hr-DLnw9bOE--VHi-1arDbIYiGuV1rlTbbHI,1466
@@ -111,8 +111,8 @@ biolib/utils/cache_state.py,sha256=u256F37QSRIVwqKlbnCyzAX4EMI-kl6Dwu6qwj-Qmag,3
 biolib/utils/multipart_uploader.py,sha256=XvGP1I8tQuKhAH-QugPRoEsCi9qvbRk-DVBs5PNwwJo,8452
 biolib/utils/seq_util.py,sha256=jC5WhH63FTD7SLFJbxQGA2hOt9NTwq9zHl_BEec1Z0c,4907
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.1.2090.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.2090.dist-info/METADATA,sha256=QIpIwVybuDIwjbpt5P49oDK52g9MBQJvKGlm5J0lVV8,1508
-pybiolib-1.1.2090.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.2090.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.2090.dist-info/RECORD,,
+pybiolib-1.1.2109.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.2109.dist-info/METADATA,sha256=Ib3gPLhMCJEEmlmAf7rgaOg4ZR2x1pQef1XCOCryito,1508
+pybiolib-1.1.2109.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.2109.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.2109.dist-info/RECORD,,