pybiolib 1.2.1389__py3-none-any.whl → 1.2.1414__py3-none-any.whl

biolib/jobs/job.py

@@ -26,7 +26,7 @@ from biolib.compute_node.utils import SystemExceptionCodeMap, SystemExceptionCod
 from biolib.jobs.job_result import JobResult
 from biolib.jobs.types import CloudJobDict, CloudJobStartedDict, JobDict
 from biolib.tables import BioLibTable
-from biolib.typing_utils import Dict, List, Optional, Union, cast
+from biolib.typing_utils import Dict, Generator, List, Optional, Tuple, Union, cast
 from biolib.utils import IS_RUNNING_IN_NOTEBOOK
 from biolib.utils.app_uri import parse_app_uri
 
@@ -493,22 +493,11 @@ class Result:
         return Result(job_dict)
 
     @staticmethod
-    def print_logs_packages(stdout_and_stderr_packages_b64):
+    def _yield_logs_packages(stdout_and_stderr_packages_b64) -> Generator[Tuple[str, bytes], None, None]:
         for stdout_and_stderr_package_b64 in stdout_and_stderr_packages_b64:
             stdout_and_stderr_package = base64.b64decode(stdout_and_stderr_package_b64)
             stdout_and_stderr = StdoutAndStderr(stdout_and_stderr_package).deserialize()
-
-            if IS_RUNNING_IN_NOTEBOOK:
-                sys.stdout.write(stdout_and_stderr.decode(encoding='utf-8', errors='replace'))
-            else:
-                sys.stdout.buffer.write(stdout_and_stderr)
-                # Note: we avoid flush() in notebook as that breaks \r handling
-                sys.stdout.buffer.flush()
-        # flush after having processed all packages
-        if IS_RUNNING_IN_NOTEBOOK:
-            sys.stdout.flush()
-        else:
-            sys.stdout.buffer.flush()
+            yield ('stdout', stdout_and_stderr)
 
     def show(self) -> None:
         self._refetch_job_dict()
@@ -518,29 +507,44 @@ class Result:
             title=f'Result: {self._uuid}',
         ).print_table()
 
-    def stream_logs(self) -> None:
+    def stream_logs(self, as_iterator: bool = False):
+        if as_iterator:
+            return self._iter_logs()
         self._stream_logs()
+        return None
 
     def _stream_logs(self, enable_print: bool = True) -> None:
+        try:
+            for stream_type, data in self._iter_logs(enable_print=enable_print):
+                if stream_type == 'stdout':
+                    if IS_RUNNING_IN_NOTEBOOK:
+                        sys.stdout.write(data.decode(encoding='utf-8', errors='replace'))
+                        # Note: we avoid flush() in notebook as that breaks \r handling
+                    else:
+                        sys.stdout.buffer.write(data)
+                        sys.stdout.buffer.flush()
+                elif stream_type == 'stderr':
+                    if IS_RUNNING_IN_NOTEBOOK:
+                        sys.stderr.write(data.decode(encoding='utf-8', errors='replace'))
+                        # Note: we avoid flush() in notebook as that breaks \r handling
+                    else:
+                        sys.stderr.buffer.write(data)
+                        sys.stderr.buffer.flush()
+        finally:
+            # Flush after having processed all packages
+            if IS_RUNNING_IN_NOTEBOOK:
+                sys.stdout.flush()
+                sys.stderr.flush()
+
+    def _iter_logs(self, enable_print: bool = True) -> Generator[Tuple[str, bytes], None, None]:
         try:
             cloud_job = self._get_cloud_job_awaiting_started()
         except CloudJobFinishedError:
             logger.info(f'--- The result {self.id} has already completed (no streaming will take place) ---')
             logger.info('--- The stdout log is printed below: ---')
-            sys.stdout.flush()
-            if IS_RUNNING_IN_NOTEBOOK:
-                sys.stdout.write(self.get_stdout().decode(encoding='utf-8', errors='replace'))
-                sys.stdout.flush()
-            else:
-                sys.stdout.buffer.write(self.get_stdout())
-                sys.stdout.buffer.flush()
+            yield ('stdout', self.get_stdout())
             logger.info('--- The stderr log is printed below: ---')
-            if IS_RUNNING_IN_NOTEBOOK:
-                sys.stderr.write(self.get_stderr().decode(encoding='utf-8', errors='replace'))
-                sys.stderr.flush()
-            else:
-                sys.stderr.buffer.write(self.get_stderr())
-                sys.stderr.buffer.flush()
+            yield ('stderr', self.get_stderr())
             logger.info(f'--- The job {self.id} has already completed. Its output was printed above. ---')
             return
 
@@ -552,7 +556,7 @@ class Result:
             logger_no_user_data.debug(f'Using cloud proxy URL from env var BIOLIB_CLOUD_BASE_URL: {compute_node_url}')
 
         if enable_print:
-            self._print_full_logs(node_url=compute_node_url)
+            yield from self._yield_full_logs(node_url=compute_node_url)
 
         final_status_messages: List[str] = []
         while True:
@@ -571,8 +575,8 @@ class Result:
                     # Print the status before writing stdout and stderr
                     logger.info(f'Cloud: {status_update["log_message"]}')
 
-            if 'stdout_and_stderr_packages_b64' and enable_print:
-                self.print_logs_packages(status_json['stdout_and_stderr_packages_b64'])
+            if enable_print:
+                yield from self._yield_logs_packages(status_json['stdout_and_stderr_packages_b64'])
 
             if 'error_code' in status_json:
                 error_code = status_json['error_code']
@@ -589,7 +593,7 @@ class Result:
 
         self.wait()  # Wait for compute node to tell the backend that the job is finished
 
-    def _print_full_logs(self, node_url: str) -> None:
+    def _yield_full_logs(self, node_url: str) -> Generator[Tuple[str, bytes], None, None]:
         try:
             response_json = HttpClient.request(url=f'{node_url}/v1/job/{self._uuid}/status/?logs=full').json()
         except Exception as error:
@@ -599,7 +603,7 @@ class Result:
         for status_update in response_json.get('previous_status_updates', []):
             logger.info(f'Cloud: {status_update["log_message"]}')
 
-        self.print_logs_packages(response_json['streamed_logs_packages_b64'])
+        yield from self._yield_logs_packages(response_json['streamed_logs_packages_b64'])
 
     def _get_cloud_job_awaiting_started(self) -> CloudJobStartedDict:
         retry_count = 0

{pybiolib-1.2.1389.dist-info → pybiolib-1.2.1414.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pybiolib
-Version: 1.2.1389
+Version: 1.2.1414
 Summary: BioLib Python Client
 License: MIT
 License-File: LICENSE

{pybiolib-1.2.1389.dist-info → pybiolib-1.2.1414.dist-info}/RECORD

@@ -145,7 +145,7 @@ biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6p
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=ePipnJs6TW84jr9iBfYYRpYuEXUVGIxaD8Z8Jf0FYIA,13909
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=X7F_jCwAwtPcI1qu-oLamZNzt1IVSIeOPWlax1ztfAM,29674
+biolib/jobs/job.py,sha256=3cUFo459O3Q3HDB3c6MTpJ-lDAyRsEi5cjnV6FA0W6g,30078
 biolib/jobs/job_result.py,sha256=Yl22Z8dc-8iKeC7Y4q7kgd08Ndajys1W1MsAbvE8wOA,5252
 biolib/jobs/types.py,sha256=rFs6bQWsNI-nb1Hu9QzOW2zFZ8bOVt7ax4UpGVASxVA,1034
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -161,8 +161,8 @@ 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=rImaghQGuIqTVWks6b9P2yKuN34uePUYPUFW_Wyoa4A,6737
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.1389.dist-info/METADATA,sha256=y8bhxtHgW135kkkPiKCE0WKPSZ4-DaEFS8aE9UAhmn0,1644
-pybiolib-1.2.1389.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-pybiolib-1.2.1389.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.1389.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.1389.dist-info/RECORD,,
+pybiolib-1.2.1414.dist-info/METADATA,sha256=Tj71O4hNuExDxY_MTxPjDUPKqMmXQgTtC2M5tcauO8g,1644
+pybiolib-1.2.1414.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+pybiolib-1.2.1414.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.1414.dist-info/licenses/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.1414.dist-info/RECORD,,