pybiolib 1.1.801__py3-none-any.whl → 1.1.809__py3-none-any.whl

biolib/cli/__init__.py

@@ -4,7 +4,7 @@ import click
 
 from biolib import utils
 from biolib.biolib_logging import logger, logger_no_user_data
-from biolib.cli import init, lfs, push, run, run_dev, start, runtime
+from biolib.cli import init, lfs, push, run, start, runtime
 
 
 @click.version_option(version=utils.BIOLIB_PACKAGE_VERSION, prog_name='pybiolib')
@@ -23,8 +23,6 @@ cli.add_command(lfs.lfs)
 cli.add_command(push.push)
 cli.add_command(run.run)
 cli.add_command(runtime.runtime)
-# TODO: Remove this function
-cli.add_command(run_dev.run_dev)  # type: ignore
 cli.add_command(start.start)
 
 # allow this script to be called without poetry in dev e.g. by an IDE debugger

biolib/compute_node/remote_host_proxy.py

@@ -248,6 +248,7 @@ http {{
             # Note: Using $1 here as URI part from regex must be used for proxy_pass
             proxy_pass               {base_url}/api/jobs/$1;
             proxy_set_header         authorization $bearer_token_on_post;
+            proxy_set_header         caller-job-uuid "{self._job_uuid}";
             proxy_set_header         cookie "";
             proxy_ssl_server_name    on;
         }}

biolib/experiments/experiment.py

@@ -76,6 +76,12 @@ class Experiment:
 
         print(f'All jobs of experiment {self.name} have finished')
 
+    def add_job(self, job_id: str) -> None:
+        api.client.patch(
+            path=f'/jobs/{job_id}/',
+            data={'experiment_uuid': self.uuid}
+        )
+
     def export_job_list(self, export_format='dicts'):
         valid_formats = ('dicts', 'dataframe')
         if export_format not in valid_formats:

{pybiolib-1.1.801.dist-info → pybiolib-1.1.809.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.801
+Version: 1.1.809
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.801.dist-info → pybiolib-1.1.809.dist-info}/RECORD

@@ -36,12 +36,11 @@ biolib/biolib_docker_client/__init__.py,sha256=aBfA6mtWSI5dBEfNNMD6bIZzCPloW4ghK
 biolib/biolib_errors.py,sha256=x1NZJrAFcwybc2VlwlIduJPsUhAV1qNbSsMaU8CpVyQ,532
 biolib/biolib_logging.py,sha256=J3E5H_LL5k6ZUim2C8gqN7E6lCBZMTpO4tnMpOPwG9U,2854
 biolib/biolib_push.py,sha256=QHAA0TJjbjEKFYlHeKX14SEyDUHP9tc0b0OX4KtqszA,10225
-biolib/cli/__init__.py,sha256=WIyZZeR264YORS8gUe6_gAJIB0b1Cgxt5wx1UhsV8k4,1034
+biolib/cli/__init__.py,sha256=nf0tgrilBU1StpK58h2YZ3LEPtce2ywW5dzQcFaBOcc,947
 biolib/cli/init.py,sha256=Rd6_zpQxQbB0UaSEBFxfsL2j64YuINilNzhDydDDBig,820
 biolib/cli/lfs.py,sha256=oYsSsHv_ZddcUN_R_SaaytvMM4QEtG3Inn5cV7zML-o,1635
 biolib/cli/push.py,sha256=imubLFA0BlXrdwHnIyaxhok6mbVQfZ5NCNNTf4c89rs,798
 biolib/cli/run.py,sha256=F7izVu0dRLS0gPD2WWhOAEv0KCWqQtyRD_zw7gMV5Gc,1309
-biolib/cli/run_dev.py,sha256=XIPiOrQUtpT82bNy923-1sPtcaeLed3wFuongPQrLqk,3765
 biolib/cli/runtime.py,sha256=Xv-nrma5xX8NidWcvbUKcUvuN5TCarZa4A8mPVmF-z0,361
 biolib/cli/start.py,sha256=CVcv5ZrqJx8vIgEfW_ls7WlU1vNer96Rvr4MjP8-SZM,1284
 biolib/cli_utils.py,sha256=uDMdbcn7NP4cBGPeGr6vtiTvy0OOCyAjdVEokSYkFIg,8947
@@ -68,7 +67,7 @@ biolib/compute_node/job_worker/job_worker.py,sha256=5K7dwCCrlogDMjOcP0sQHhjwR-zZ
 biolib/compute_node/job_worker/large_file_system.py,sha256=K_tyz01ZLvGim_M7ox-ecKTOosaguLHDuSZX4aHJYZw,10277
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/utils.py,sha256=wgxcIA8yAhUPdCwyvuuJ0JmreyWmmUoBO33vWtG60xg,1282
-biolib/compute_node/remote_host_proxy.py,sha256=BK4sd_Yrwvs8eA2hmx6U0GKs-rTm4Vmuro855jpYu6o,12727
+biolib/compute_node/remote_host_proxy.py,sha256=tKtYdpJNoNTSN3tH2Im_U33uUXsbj1WB1EOrxXi50Rg,12800
 biolib/compute_node/socker_listener_thread.py,sha256=T5_UikA3MB9bD5W_dckYLPTgixh72vKUlgbBvj9dbM0,1601
 biolib/compute_node/socket_sender_thread.py,sha256=YgamPHeUm2GjMFGx8qk-99WlZhEs-kAb3q_2O6qByig,971
 biolib/compute_node/utils.py,sha256=WuCipw4_0c33hzjmJnr53MuXo_R8TEowy5A1QF1Eb3c,4434
@@ -79,7 +78,7 @@ biolib/compute_node/webserver/webserver_types.py,sha256=Vmt1ZDecYhGBVEYWcW1DVxee
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=JngK_wVADJnrX04KZ99o4BzZWaozZxYl1wQElwkLYYo,9900
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-biolib/experiments/experiment.py,sha256=mzO-VgWkPfqMF7z2DnESNcZo8zUHR4dXIySEr8H4gII,5773
+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=cCR8XGYAqU22tFr1I7g09Pj65I-OqN95iSo9K5Nah7w,14007
@@ -105,8 +104,8 @@ biolib/validators/validate_argument.py,sha256=B-tqgMgXuTvJLhaMWcBTUKw18L5brJtIdf
 biolib/validators/validate_module.py,sha256=aHe0YAWFSrMbZNw-h64oweqruDS-k7KOUzK1ECpG8Wg,13298
 biolib/validators/validate_zip_file.py,sha256=2j8kJ1WF2u5OyMkfEDCoU_BvOtr8gLPWTtsmUG0zQ5g,1655
 biolib/validators/validator_utils.py,sha256=2QCJWdKiLTUHsvjDidrXKBjH95kKsEmFwd17muTGL0M,2135
-pybiolib-1.1.801.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.801.dist-info/METADATA,sha256=pGZCb5UhynRrIKd8UENHOkRGrXE8cutujDU2qnJW_Hw,1651
-pybiolib-1.1.801.dist-info/WHEEL,sha256=vVCvjcmxuUltf8cYhJ0sJMRDLr1XsPuxEId8YDzbyCY,88
-pybiolib-1.1.801.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.801.dist-info/RECORD,,
+pybiolib-1.1.809.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.809.dist-info/METADATA,sha256=RM5_L9xRwOjavPyJoEecwpYO3YDUni5pBCiHWxSCIB0,1651
+pybiolib-1.1.809.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+pybiolib-1.1.809.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.809.dist-info/RECORD,,

{pybiolib-1.1.801.dist-info → pybiolib-1.1.809.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.4.0
+Generator: poetry-core 1.5.2
 Root-Is-Purelib: true
 Tag: py3-none-any

biolib/cli/run_dev.py

@@ -1,95 +0,0 @@
-# type: ignore
-# TODO: Remove this file and function
-import sys
-import click
-from docker.errors import ImageNotFound  # type: ignore
-
-from biolib import utils, cli_utils
-from biolib.app.utils import run_job
-from biolib.biolib_binary_format import ModuleInput
-from biolib.biolib_docker_client import BiolibDockerClient
-from biolib.biolib_logging import logger, logger_no_user_data
-from biolib.biolib_api_client import CreatedJobDict
-from biolib.cli_utils import BiolibValidationError
-from biolib.typing_utils import Tuple
-from biolib.validators.validate_zip_file import validate_zip_file  # type: ignore
-
-
-@click.command(
-    context_settings=dict(ignore_unknown_options=True, allow_interspersed_args=False),
-    help='Run an application from a local directory',
-    hidden=True,
-)
-@click.argument('path', required=True)
-@click.argument('args', nargs=-1, type=click.UNPROCESSED)
-def run_dev(path: str, args: Tuple[str]) -> None:
-    app_path = cli_utils.validate_and_get_app_path(path)
-    logger.info(f'Running BioLib application in local directory {app_path}...')
-    tmp_directory, source_files_zip_path = cli_utils.create_temporary_directory_with_source_files_zip(app_path)
-
-    try:
-        validate_zip_file(source_files_zip_path, app_path)
-        yaml_data = cli_utils.get_yaml_data(app_path)
-        cli_utils.validate_yaml_config(yaml_data, source_files_zip_path)
-        app_version_mocked = cli_utils.get_mocked_app_version_from_yaml(yaml_data, source_files_zip_path)
-
-        for module in app_version_mocked['modules']:
-            try:
-                BiolibDockerClient.get_docker_client().images.get(module['image_uri'])
-            except ImageNotFound:
-                raise Exception(
-                    f"Could not find local docker image {module['image_uri']} specified in .biolib/config.yml"
-                ) from None
-
-        args = cli_utils.validate_and_get_args(list(args))
-        files_dict, args = cli_utils.get_files_dict_and_file_args(files=None, args=args)
-
-        def _get_stdin():
-            stdin = None
-            if not sys.stdin.isatty() and not utils.IS_DEV:
-                stdin = sys.stdin.read()
-            return stdin
-
-        module_input_serialized = ModuleInput().serialize(
-            stdin=_get_stdin() or b'',
-            files=files_dict,
-            arguments=args,
-        )
-
-        module_output = run_job(
-            module_input_serialized=module_input_serialized,
-            job=CreatedJobDict(
-                app_version=app_version_mocked,
-                arguments_override_command=False,
-                auth_token='',
-                caller_job=None,
-                created_at='',
-                federated_job_uuid=None,
-                public_id=utils.RUN_DEV_JOB_ID,
-                remote_hosts_with_warning=[],
-                state='in_progress',
-                user_id=None,
-            ),
-            force_local=True,
-        )
-
-        cli_utils.write_output_files(module_output['files'])  # type: ignore
-
-        print(cli_utils.get_pretty_print_module_output_string(
-            exitcode=module_output['exit_code'],  # type: ignore
-            stderr=module_output['stderr'],  # type: ignore
-            stdout=module_output['stdout'],  # type: ignore
-        ))
-
-    except Exception as exception:
-        # Exit on BiolibValidationError as we have already printed the validation errors
-        if isinstance(exception, BiolibValidationError):
-            logger_no_user_data.error('Validation check failed for config file at .biolib/config.yml')
-            exit(1)
-        raise exception
-
-    finally:
-        try:
-            tmp_directory.cleanup()
-        except IOError:
-            logger_no_user_data.error('Failed to clean up temporary source files zip directory')