pybiolib 1.1.2090__tar.gz → 1.1.2109__tar.gz

{pybiolib-1.1.2090 → pybiolib-1.1.2109}/PKG-INFO

@@ -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-1.1.2109/biolib/cli/data_record.py

@@ -0,0 +1,79 @@
+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.typing_utils import Optional
+
+
+@click.group(help='Data Records')
+def data_record() -> None:
+    logger.configure(default_log_level=logging.INFO)
+    logger_no_user_data.configure(default_log_level=logging.INFO)
+
+
+@data_record.command(help='Create a Data Record')
+@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('--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')
+@click.argument('uri', required=True)
+@click.option('--file', required=False, type=str)
+@click.option('--path-filter', required=False, type=str, hide_input=True)
+def download(uri: str, file: Optional[str], path_filter: Optional[str]) -> None:
+    record = DataRecord.get_by_uri(uri=uri)
+    if file is not None:
+        try:
+            file_obj = [file_obj for file_obj in record.list_files() if file_obj.path == file][0]
+        except IndexError:
+            raise Exception('File not found in data record') from None
+
+        assert not os.path.exists(file_obj.name), 'File already exists in current directory'
+        with open(file_obj.name, 'wb') as file_handle:
+            file_handle.write(file_obj.get_data())
+
+    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']}")

{pybiolib-1.1.2090 → pybiolib-1.1.2109}/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

{pybiolib-1.1.2090 → pybiolib-1.1.2109}/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 → pybiolib-1.1.2109}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.2090"
+version = "1.1.2109"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"

pybiolib-1.1.2090/biolib/cli/data_record.py

@@ -1,44 +0,0 @@
-import logging
-import os
-
-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
-
-
-@click.group(help='Data Records')
-def data_record() -> None:
-    logger.configure(default_log_level=logging.INFO)
-    logger_no_user_data.configure(default_log_level=logging.INFO)
-
-
-@data_record.command(help='Create a Data Record')
-@click.option('--destination', type=str, 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)
-
-
-@data_record.command(help='Download files from a Data Record')
-@click.argument('uri', required=True)
-@click.option('--file', required=False, type=str)
-@click.option('--path-filter', required=False, type=str, hide_input=True)
-def download(uri: str, file: Optional[str], path_filter: Optional[str]) -> None:
-    record = DataRecord.get_by_uri(uri=uri)
-    if file is not None:
-        try:
-            file_obj = [file_obj for file_obj in record.list_files() if file_obj.path == file][0]
-        except IndexError:
-            raise Exception('File not found in data record') from None
-
-        assert not os.path.exists(file_obj.name), 'File already exists in current directory'
-        with open(file_obj.name, 'wb') as file_handle:
-            file_handle.write(file_obj.get_data())
-
-    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)