pybiolib 1.1.1412__py3-none-any.whl → 1.1.1420__py3-none-any.whl

biolib/biolib_binary_format/module_input.py

@@ -1,4 +1,11 @@
 from biolib.biolib_binary_format.base_bbf_package import BioLibBinaryFormatBasePackage
+from biolib.typing_utils import TypedDict, Dict, List
+
+
+class ModuleInputDict(TypedDict):
+    stdin: bytes
+    files: Dict[str, bytes]
+    arguments: List[str]
 
 
 class ModuleInput(BioLibBinaryFormatBasePackage):
@@ -36,7 +43,7 @@ class ModuleInput(BioLibBinaryFormatBasePackage):
 
         return bbf_data
 
-    def deserialize(self):
+    def deserialize(self) -> ModuleInputDict:
         version = self.get_data(1, output_type='int')
         package_type = self.get_data(1, output_type='int')
         self.check_version_and_type(version=version, package_type=package_type, expected_package_type=self.package_type)
@@ -62,4 +69,4 @@ class ModuleInput(BioLibBinaryFormatBasePackage):
             data = self.get_data(data_len)
             files[path] = bytes(data)
 
-        return {'stdin': stdin, 'arguments': arguments, 'files': files}
+        return ModuleInputDict(stdin=stdin, arguments=arguments, files=files)

biolib/jobs/job.py

@@ -9,7 +9,7 @@ from urllib.parse import urlparse
 import requests
 from biolib import api, utils
 from biolib.biolib_api_client.biolib_job_api import BiolibJobApi
-from biolib.biolib_binary_format import LazyLoadedFile, ModuleOutputV2, ModuleInput
+from biolib.biolib_binary_format import LazyLoadedFile, ModuleOutputV2, ModuleInput, ModuleInputDict
 from biolib.biolib_binary_format.stdout_and_stderr import StdoutAndStderr
 from biolib.biolib_errors import BioLibError, CloudJobFinishedError
 from biolib.biolib_logging import logger, logger_no_user_data
@@ -37,6 +37,7 @@ class Job:
         self._job_dict: JobDict = job_dict
         self._job_dict_last_fetched_at: datetime = datetime.utcnow()
         self._result: Optional[JobResult] = None
+        self._cached_input_arguments: Optional[List[str]] = None
 
     def __str__(self):
         return f"Job for {self._job_dict['app_uri']} created at {self._job_dict['created_at']} ({self._uuid})"
@@ -114,27 +115,29 @@ class Job:
     def get_exit_code(self) -> int:
         return self.result.get_exit_code()
 
-    def save_input_files(self, output_dir: str) -> None:
+    def _get_module_input(self) -> ModuleInputDict:
         self._refetch_job_dict()
-        logger.info('Downloading input files...')
-        try:
-            presigned_download_url = BiolibJobApi.get_job_storage_download_url(
-                job_uuid=self._job_dict['uuid'],
-                job_auth_token=self._job_dict['auth_token'],
-                storage_type='input',
-            )
-            response = requests.get(url=presigned_download_url)
-            response.raise_for_status()
-            module_input_serialized: bytes = response.content
-        except Exception as error:
-            # TODO: Improve error handling and messages
-            raise error
+        presigned_download_url = BiolibJobApi.get_job_storage_download_url(
+            job_uuid=self._job_dict['uuid'],
+            job_auth_token=self._job_dict['auth_token'],
+            storage_type='input',
+        )
+        response = requests.get(url=presigned_download_url)
+        response.raise_for_status()
+        module_input_serialized: bytes = response.content
+        return ModuleInput(module_input_serialized).deserialize()
 
-        try:
-            module_input = ModuleInput(module_input_serialized).deserialize()
-        except Exception as error:
-            # TODO: Improve error handling and messages
-            raise error
+    def get_input_arguments(self) -> List[str]:
+        if self._cached_input_arguments is None:
+            logger.debug('Fetching input arguments...')
+            module_input = self._get_module_input()
+            self._cached_input_arguments = module_input['arguments']
+
+        return self._cached_input_arguments
+
+    def save_input_files(self, output_dir: str) -> None:
+        logger.info('Downloading input files...')
+        module_input = self._get_module_input()
 
         files = module_input['files'].items()
         logger.info(f'Saving input {len(files)} files to "{output_dir}"...')

{pybiolib-1.1.1412.dist-info → pybiolib-1.1.1420.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1412
+Version: 1.1.1420
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1412.dist-info → pybiolib-1.1.1420.dist-info}/RECORD

@@ -21,7 +21,7 @@ biolib/biolib_api_client/user_state.py,sha256=XcgWV-MgVk88mIlMmnu8yHxMu8OCaw8o0t
 biolib/biolib_binary_format/__init__.py,sha256=HMl5SdX_VUWE4OQzi4Jf_yFvC7b0bSPOGPHYi9dWM2Q,185
 biolib/biolib_binary_format/base_bbf_package.py,sha256=vxRV4iKy0dXeDOlFWnMFI0hGnDBYDH5Cgh5gAfuObt8,959
 biolib/biolib_binary_format/file_in_container.py,sha256=sgj0YWPuWhNOiFsVf4X7Sf2AYO4kGCHj4DSUceCifJ0,2753
-biolib/biolib_binary_format/module_input.py,sha256=E-mvq26NFpYM7fqMMj8Nrpqxezy4CWRA1OS3hJK1kk0,2603
+biolib/biolib_binary_format/module_input.py,sha256=led2QhHeec_ymBPw5uEn3_3vJKI-1T8zrFQGqwEWLMY,2788
 biolib/biolib_binary_format/module_output_v2.py,sha256=J5ZO5gCSeudpE12EVDrjYrNTS2DwgszY-SVXT7Qjuyg,5913
 biolib/biolib_binary_format/remote_endpoints.py,sha256=LgWd_cewZK4ncPR8303GM_PmIEZZJ5RQatJ_NSXUgbU,1306
 biolib/biolib_binary_format/remote_stream_seeker.py,sha256=uyi6kJBU1C1DWfiuR0kRUQIY7nalG7ocgwgngd3Ul4U,1999
@@ -76,7 +76,7 @@ biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 biolib/experiments/experiment.py,sha256=NjJOFktfTbgHNtIDavyQP_uL_-gSGwYHfycybPLJRKU,5939
 biolib/experiments/types.py,sha256=n9GxdFA7cLMfHvLLqLmZzX31ELeSSkMXFoEEdFsdWGY,171
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=Rthdl-t8Md8z1NohkHr9E6SYoWNTw1GLakCo0FXeC2M,14708
+biolib/jobs/job.py,sha256=Alshkwmpnv_15zKY2hZ_lFeFV2ShycJO5C3dhZsgKD4,14910
 biolib/jobs/job_result.py,sha256=8GasUmUXD8SjUYrE2N-HrDx7-AI6TEkFONH8H91t01Q,4913
 biolib/jobs/types.py,sha256=kn4Vc0fDi6jFVcjpcKH6AYFKXkVA_CaRvtmsJoSyr0c,905
 biolib/lfs/__init__.py,sha256=wspftSqe_x7xPMZbeW8mcIBuxbHFCiFI3V4TuZU4nZ4,193
@@ -96,8 +96,8 @@ biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3
 biolib/utils/multipart_uploader.py,sha256=Bf09MJcIOBwzG8L1i5UeQ2cNcYohxklhhWWAMpnE41I,9671
 biolib/utils/seq_util.py,sha256=QRLYIPg1yM_LF9bFuM-Ow14gTHoG3rOK6CeGHD705qw,2612
 biolib/utils/zip/remote_zip.py,sha256=NCdUnVbGCv7SfXCI-yVU-is_OnyWmLAnVpIdSvo-W4k,23500
-pybiolib-1.1.1412.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1412.dist-info/METADATA,sha256=HmeOYQ7UPCxZbKgdzhaknb4djL7EWPzezWOrk0wVJiE,1492
-pybiolib-1.1.1412.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
-pybiolib-1.1.1412.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1412.dist-info/RECORD,,
+pybiolib-1.1.1420.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1420.dist-info/METADATA,sha256=gvld8xTOveRhdDjevpxT-qmRc4uDbWSylZjwzMdiC7U,1492
+pybiolib-1.1.1420.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
+pybiolib-1.1.1420.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1420.dist-info/RECORD,,