pybiolib 1.1.1921__py3-none-any.whl → 1.1.1926__py3-none-any.whl

biolib/_internal/runtime.py

@@ -9,6 +9,7 @@ class RuntimeJobDataDict(TypedDict):
     job_requested_machine: str
     job_uuid: str
     job_auth_token: str
+    app_uri: str
 
 
 class BioLibRuntimeError(Exception):
@@ -40,6 +41,10 @@ class Runtime:
     def get_job_requested_machine() -> str:
         return Runtime._get_job_data()['job_requested_machine']
 
+    @staticmethod
+    def get_app_uri() -> str:
+        return Runtime._get_job_data()['app_uri']
+
     @staticmethod
     def set_main_result_prefix(result_prefix: str) -> None:
         job_data = Runtime._get_job_data()
@@ -49,6 +54,12 @@ class Runtime:
             path=f"/jobs/{job_data['job_uuid']}/main_result/",
         )
 
+    @staticmethod
+    def create_result_note(note: str) -> None:
+        job_id = Runtime.get_job_id()
+        # Authentication is added by app caller proxy in compute node
+        api.client.patch(data={'note': note}, path=f'/jobs/{job_id}/notes/')
+
     @staticmethod
     def _try_to_get_job_data() -> Optional[RuntimeJobDataDict]:
         if not Runtime._job_data:

biolib/biolib_api_client/job_types.py

@@ -15,6 +15,7 @@ class JobState(Enum):
 
 
 class _Job(TypedDict):
+    app_uri: str
     app_version: AppVersionOnJob
     arguments_override_command: bool
     auth_token: str
@@ -22,10 +23,10 @@ class _Job(TypedDict):
     created_at: str
     federated_job_uuid: Optional[str]
     public_id: str
-    uuid: str
     remote_hosts_with_warning: List[RemoteHost]
     state: str
     user_id: Optional[str]
+    uuid: str
 
 
 # type optional keys with total=False

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -275,6 +275,7 @@ class DockerExecutor:
                 job_requested_machine=self._options['job']['requested_machine'],
                 job_uuid=self._options['job']['public_id'],
                 job_auth_token=self._options['job']['auth_token'],
+                app_uri=self._options['job']['app_uri'],
             )
             secrets: Dict[str, str] = dict(
                 **module.get('secrets', {}),

biolib/compute_node/remote_host_proxy.py

@@ -1,21 +1,20 @@
 import io
-import tarfile
 import subprocess
+import tarfile
 import time
 
-from docker.models.containers import Container  # type: ignore
 from docker.errors import ImageNotFound  # type: ignore
+from docker.models.containers import Container  # type: ignore
 from docker.models.images import Image  # type: ignore
 from docker.models.networks import Network  # type: ignore
 
 from biolib import utils
-from biolib.biolib_errors import BioLibError
-from biolib.compute_node.cloud_utils import CloudUtils
-from biolib.typing_utils import Optional, List
-from biolib.biolib_api_client import RemoteHost
+from biolib.biolib_api_client import BiolibApiClient, RemoteHost
 from biolib.biolib_docker_client import BiolibDockerClient
+from biolib.biolib_errors import BioLibError
 from biolib.biolib_logging import logger_no_user_data
-from biolib.biolib_api_client import BiolibApiClient
+from biolib.compute_node.cloud_utils import CloudUtils
+from biolib.typing_utils import List, Optional
 
 
 # Prepare for remote hosts with specified port
@@ -24,31 +23,25 @@ class RemoteHostExtended(RemoteHost):
 
 
 class RemoteHostProxy:
-
     def __init__(
-            self,
-            remote_host: RemoteHost,
-            public_network: Network,
-            internal_network: Optional[Network],
-            job_id: str,
-            ports: List[int],
-            can_push_data_record_for_user: bool,
+        self,
+        remote_host: RemoteHost,
+        public_network: Network,
+        internal_network: Optional[Network],
+        job_id: str,
+        ports: List[int],
+        can_push_data_record_for_user: bool,
     ):
         self._can_push_data_record_for_user: bool = can_push_data_record_for_user
         self.is_app_caller_proxy = remote_host['hostname'] == 'AppCallerProxy'
-
-        # Default to port 443 for now until backend serves remote_hosts with port specified
-        self._remote_host: RemoteHostExtended = RemoteHostExtended(
-            hostname=remote_host['hostname'],
-            ports=ports
-        )
+        self._remote_host: RemoteHostExtended = RemoteHostExtended(hostname=remote_host['hostname'], ports=ports)
         self._public_network: Network = public_network
         self._internal_network: Optional[Network] = internal_network
 
         if not job_id:
             raise Exception('RemoteHostProxy missing argument "job_id"')
 
-        self._name = f"biolib-remote-host-proxy-{job_id}-{self.hostname}"
+        self._name = f'biolib-remote-host-proxy-{job_id}-{self.hostname}'
         self._job_uuid = job_id
         self._container: Optional[Container] = None
         self._enclave_traffic_forwarder_processes: List[subprocess.Popen] = []
@@ -165,15 +158,19 @@ class RemoteHostProxy:
                 else:
                     raise BioLibError('Calling apps inside apps is not supported in local compute environment')
 
+            compute_node_uuid: Optional[str] = None
+            compute_node_auth_token: Optional[str] = None
             if utils.IS_RUNNING_IN_CLOUD:
                 config = CloudUtils.get_webserver_config()
+                compute_node_uuid = config['compute_node_info']['public_id']
+                compute_node_auth_token = config['compute_node_info']['auth_token']
                 s3_results_bucket_name = config['s3_general_storage_bucket_name']
                 s3_results_base_url = f'https://{s3_results_bucket_name}.s3.amazonaws.com'
             else:
                 if base_url in ('https://biolib.com', 'https://staging-elb.biolib.com'):
                     s3_results_base_url = 'https://biolib-cloud-api.s3.amazonaws.com'
                 else:
-                    raise BioLibError("Calling apps inside apps locally is only supported on biolib.com")
+                    raise BioLibError('Calling apps inside apps locally is only supported on biolib.com')
 
             # TODO: Get access_token from new API class instead
             access_token = BiolibApiClient.get().access_token
@@ -287,6 +284,17 @@ http {{
             proxy_ssl_server_name    on;
         }}
 
+        location ~ "^/api/jobs/{self._job_uuid}/notes/$" {{
+            # Note: Using $1 here as URI part from regex must be used for proxy_pass
+            proxy_pass               {base_url}/api/{self._job_uuid}/notes/$1;
+            proxy_set_header         authorization "";
+            proxy_set_header         job-auth-token "";
+            proxy_set_header         compute-node-auth-token "{compute_node_auth_token}";
+            proxy_set_header         compute-node-uuid "{compute_node_uuid}";
+            proxy_set_header         cookie "";
+            proxy_ssl_server_name    on;
+        }}
+
         location /api/lfs/ {{
             proxy_pass               {base_url}/api/lfs/;
             proxy_set_header         authorization {'$bearer_token_on_post_and_get' if self._can_push_data_record_for_user else '""'};
@@ -345,13 +353,13 @@ http {{
 }}
 '''
         else:
-            nginx_config = '''
+            nginx_config = """
 events {}
 error_log /dev/stdout info;
 stream {
-    resolver 127.0.0.11 valid=30s;'''
+    resolver 127.0.0.11 valid=30s;"""
             for idx, upstream_server_port in enumerate(upstream_server_ports):
-                nginx_config += f'''
+                nginx_config += f"""
     map "" $upstream_{idx} {{
         default {upstream_server_name}:{upstream_server_port};
     }}
@@ -364,11 +372,11 @@ stream {
     server {{
         listen          {self._remote_host['ports'][idx]} udp;
         proxy_pass      $upstream_{idx};
-    }}'''
+    }}"""
 
-            nginx_config += '''
+            nginx_config += """
 }
-'''
+"""
 
         nginx_config_bytes = nginx_config.encode()
         tarfile_in_memory = io.BytesIO()

{pybiolib-1.1.1921.dist-info → pybiolib-1.1.1926.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1921
+Version: 1.1.1926
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1921.dist-info → pybiolib-1.1.1926.dist-info}/RECORD

@@ -7,7 +7,7 @@ biolib/_internal/data_record/data_record.py,sha256=ctijrrZ-LfUxtwzS8PEVa1VBuBLVW
 biolib/_internal/data_record/remote_storage_endpoint.py,sha256=LPq8Lr5FhKF9_o5K-bUdT7TeLe5XFUD0AAeTkNEVZug,1133
 biolib/_internal/http_client.py,sha256=38PHvRkqdjcOgRXkWU7UoYCQxHMX0eKpuwKhudDupII,4525
 biolib/_internal/push_application.py,sha256=H1PGNtVJ0vRC0li39gFMpPpjm6QeZ8Ob-7cLkLmxS_Y,10009
-biolib/_internal/runtime.py,sha256=un18gmB2wFOXVjKca1Oe6mZI-xGydz8C8seScNvnC2s,2197
+biolib/_internal/runtime.py,sha256=UbRGWLQHB5-OrPGgKDGpXFchB35jc02IdjgNUWkoW1E,2564
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
 biolib/api/__init__.py,sha256=iIO8ZRdn7YDhY5cR47-Wo1YsNOK8H6RN6jn8yor5WJI,137
 biolib/api/client.py,sha256=MtDkH2Amr2Fko-bCR5DdookJu0yZ1q-6K_PPg4KK_Ek,2941
@@ -21,7 +21,7 @@ biolib/biolib_api_client/auth.py,sha256=kjm0ZHnH3I8so3su2sZbBxNHYp-ZUdrZ5lwQ0K36
 biolib/biolib_api_client/biolib_app_api.py,sha256=DndlVxrNTes6DOaWyMINLGZQCRMWVvR7gwt5HVlyf5Y,4240
 biolib/biolib_api_client/biolib_job_api.py,sha256=IpFahcRzm7GNy8DJ-XHYe-x7r4Voba8o22IXw5puHn8,6782
 biolib/biolib_api_client/common_types.py,sha256=RH-1KNHqUF-EkTpfPOSTt5Mq1GPdfju_cqXDesscO1I,123
-biolib/biolib_api_client/job_types.py,sha256=XlDIxijxymLoJcClXhl91h1E4b2fT3pszO9wjlssD4A,1284
+biolib/biolib_api_client/job_types.py,sha256=MUzXv7nCsoLiPxdC3D4mZe9a4xTeq7FgxTElLVwVhnw,1301
 biolib/biolib_api_client/lfs_types.py,sha256=xaGjE-yUyNVM3LyKdslJn5ZXWp6_kVCd4o-ch8Czfm4,227
 biolib/biolib_api_client/user_state.py,sha256=XcgWV-MgVk88mIlMmnu8yHxMu8OCaw8o0tk7TVo5Hcg,637
 biolib/biolib_binary_format/__init__.py,sha256=HMl5SdX_VUWE4OQzi4Jf_yFvC7b0bSPOGPHYi9dWM2Q,185
@@ -59,7 +59,7 @@ 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=n4BEn-bdL10uVvMDwBazK14NY25Fy_IhKY1fNRoX8LI,26455
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=Mh1Vnamq68iE_Vvd4WlrmY0CnDVW_4QTdVJoTJJyGsE,26512
 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
@@ -71,7 +71,7 @@ biolib/compute_node/job_worker/large_file_system.py,sha256=XXqRlVtYhs-Ji9zQGIk5K
 biolib/compute_node/job_worker/mappings.py,sha256=Z48Kg4nbcOvsT2-9o3RRikBkqflgO4XeaWxTGz-CNvI,2499
 biolib/compute_node/job_worker/utilization_reporter_thread.py,sha256=7tm5Yk9coqJ9VbEdnO86tSXI0iM0omwIyKENxdxiVXk,8575
 biolib/compute_node/job_worker/utils.py,sha256=wgxcIA8yAhUPdCwyvuuJ0JmreyWmmUoBO33vWtG60xg,1282
-biolib/compute_node/remote_host_proxy.py,sha256=spjYghbqwX3dFrmedGvXZGXEsnwop1IbbyrXTv1PWz0,15080
+biolib/compute_node/remote_host_proxy.py,sha256=OjMtBePFyfDwMy9TKEiJcHc1eVyg_aDfwHxS6UZ3VCw,15763
 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=M7i_WTyxbFM3Lri9RWZ_8FeQNYrQIWpKGLfp2I55oeY,4677
@@ -105,8 +105,8 @@ 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-1.1.1921.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1921.dist-info/METADATA,sha256=quYP4m07RNqDCIBxj-UafoDq46C2e63zXhXD1QLGhiQ,1508
-pybiolib-1.1.1921.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.1.1921.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1921.dist-info/RECORD,,
+pybiolib-1.1.1926.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1926.dist-info/METADATA,sha256=zQeAwzfJS-WmGU11lXt6XUKjuTccoiGj6yIwDY5Fm5U,1508
+pybiolib-1.1.1926.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.1.1926.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1926.dist-info/RECORD,,