pybiolib 1.2.211__py3-none-any.whl → 1.2.218__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -122,7 +122,7 @@ class DockerExecutor:
                 time.sleep(5 * retry_count)
             try:
                 start_time = time.time()
-                if utils.IS_RUNNING_IN_CLOUD and not self._options['job'].get('federated_job_uuid'):
+                if utils.IS_RUNNING_IN_CLOUD:
                     DockerImageCache().get(
                         image_uri=self._absolute_image_uri,
                         estimated_image_size_bytes=estimated_image_size_bytes,
@@ -133,7 +133,7 @@ class DockerExecutor:
                     try:
                         docker_client.images.get(self._absolute_image_uri)
                     except ImageNotFound:
-                        job_uuid = self._options['job'].get('federated_job_uuid') or self._options['job']['public_id']
+                        job_uuid = self._options['job']['public_id']
                         docker_client.images.pull(
                             self._absolute_image_uri,
                             auth_config={'username': 'biolib', 'password': f',{job_uuid}'},

biolib/compute_node/webserver/webserver.py

@@ -19,7 +19,11 @@ from biolib.typing_utils import Optional
 
 app = Flask(__name__)
 
-biolib_tmp_dir = tempfile.TemporaryDirectory()
+if utils.IS_RUNNING_IN_CLOUD:
+    _BIOLIB_TMP_DIR = '/biolib/tmp'
+    os.makedirs(_BIOLIB_TMP_DIR, exist_ok=True)
+else:
+    _BIOLIB_TMP_DIR = tempfile.TemporaryDirectory().name
 
 
 @app.route('/hello/')
@@ -41,7 +45,7 @@ def save_job():
         return jsonify({'job': 'Invalid job'}), 400
 
     job_id = saved_job['job']['public_id']
-    job_temporary_dir = os.path.join(biolib_tmp_dir.name, job_id)
+    job_temporary_dir = os.path.join(_BIOLIB_TMP_DIR, job_id)
     os.makedirs(job_temporary_dir)
     saved_job['BASE_URL'] = BiolibApiClient.get().base_url
     saved_job['job_temporary_dir'] = job_temporary_dir

biolib/utils/__init__.py

@@ -87,12 +87,17 @@ def _download_chunk(input_tuple: DownloadChunkInputTuple) -> bytes:
     byte_range, presigned_url = input_tuple
     start, end = byte_range
 
-    response = HttpClient.request(
-        url=presigned_url,
-        headers={'range': f'bytes={start}-{end}'},
-        timeout_in_seconds=300,  # timeout after 5 min
-        retries=10,
-    )
+    try:
+        response = HttpClient.request(
+            url=presigned_url,
+            headers={'range': f'bytes={start}-{end}'},
+            timeout_in_seconds=300,  # timeout after 5 min
+            retries=20,
+        )
+    except Exception as exception:
+        logger_no_user_data.exception("Hit error downloading chunk")
+        logger_no_user_data.error(exception)
+        raise exception
     logger_no_user_data.debug(f'Returning raw data for part {start}')
     return response.content
 

{pybiolib-1.2.211.dist-info → pybiolib-1.2.218.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.2.211
+Version: 1.2.218
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.2.211.dist-info → pybiolib-1.2.218.dist-info}/RECORD

@@ -78,7 +78,7 @@ 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=SbqzggvXq8FiTc96umOVbIQmaYQHmhRzdW3-i7JKVIU,28044
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=Rt_kpqpBmn6Ut4h-46nqc-g4Qhs4gtbNwEpLiOKOFOM,27939
 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
@@ -96,7 +96,7 @@ biolib/compute_node/socket_sender_thread.py,sha256=YgamPHeUm2GjMFGx8qk-99WlZhEs-
 biolib/compute_node/utils.py,sha256=M7i_WTyxbFM3Lri9RWZ_8FeQNYrQIWpKGLfp2I55oeY,4677
 biolib/compute_node/webserver/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/compute_node/webserver/gunicorn_flask_application.py,sha256=jPfR_YvNBekLUXWo_vHFV-FIwlb8s8tacKmGHvh93qc,914
-biolib/compute_node/webserver/webserver.py,sha256=15PkRyhtdtSgFDxa0z78aPO4ciZURsFqJYi-HtUmZF8,6494
+biolib/compute_node/webserver/webserver.py,sha256=o4kOAStsqThUtKlnRE-U5TP0JIYntuySDjU7PH310xg,6620
 biolib/compute_node/webserver/webserver_types.py,sha256=2t8EaFKESnves3BA_NBdnS2yAdo1qwamCFHiSt888nE,380
 biolib/compute_node/webserver/webserver_utils.py,sha256=XWvwYPbWNR3qS0FYbLLp-MDDfVk0QdaAmg3xPrT0H2s,4234
 biolib/compute_node/webserver/worker_thread.py,sha256=GRRBUqXdMKvbjyLQhYlqGIbFKeU2iiEXIe5IXi9wgdg,11806
@@ -114,14 +114,14 @@ biolib/templates/example_app.py,sha256=EB3E3RT4SeO_ii5nVQqJpi5KDGNE_huF1ub-e5ZFv
 biolib/typing_utils.py,sha256=ntzrlyTkUaO2OtccLYzCAGztGdca0WT5fikJUmSkT-Y,148
 biolib/user/__init__.py,sha256=Db5wtxLfFz3ID9TULSSTo77csw9tO6RtxMRvV5cqKEE,39
 biolib/user/sign_in.py,sha256=XTAmRPKfmg7VAaB8cT5wcmfxoPXeHqY8LmDiADF7zbw,2064
-biolib/utils/__init__.py,sha256=fwjciJyJicvYyZcVTzfDBgD0SKY13DeXqvTeG4qZIy8,5548
+biolib/utils/__init__.py,sha256=rOUFayiY9h23ytSZgCNc7kEHorqFWxvYmt789Zb5mCM,5754
 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=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.211.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.211.dist-info/METADATA,sha256=b8uo9Ku57bG5-2iBqGHGlwwc2XUG7wbMTP1Y7sIn9K8,1558
-pybiolib-1.2.211.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
-pybiolib-1.2.211.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.211.dist-info/RECORD,,
+pybiolib-1.2.218.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.218.dist-info/METADATA,sha256=j5zDe_qsU-YkwN5wtvp2Sw_B85g67nzkQ7SaU94gn6o,1558
+pybiolib-1.2.218.dist-info/WHEEL,sha256=Nq82e9rUAnEjt98J6MlVmMCZb-t9cYE2Ir1kpBmnWfs,88
+pybiolib-1.2.218.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.218.dist-info/RECORD,,