pybiolib 1.2.144.dev1__py3-none-any.whl → 1.2.158.dev1__py3-none-any.whl

biolib/_runtime/runtime.py

@@ -1,10 +1,13 @@
 import json
+import logging
+import os
 import re
 from typing import Optional
 
 from biolib import api
 from biolib._internal.runtime import BioLibRuntimeError, BioLibRuntimeNotRecognizedError, RuntimeJobDataDict
 from biolib.typing_utils import cast
+from biolib.utils.seq_util import SeqUtil
 
 
 class Runtime:
@@ -54,6 +57,32 @@ class Runtime:
             path=f"/jobs/{job_data['job_uuid']}/main_result/",
         )
 
+    @staticmethod
+    def set_result_name_prefix(result_prefix: str) -> None:
+        Runtime.set_main_result_prefix(result_prefix)
+
+    @staticmethod
+    def set_result_name_prefix_from_fasta(path_to_fasta: str) -> None:
+        """
+        Set BioLib result name to FASTA file name (excluding file extension) or,
+        if detecting a BioLib generated name, use ID of the first sequence in the fasta file
+        """
+
+        def file_path_to_stem(file_path):
+            return os.path.splitext(os.path.basename(file_path))[0]
+
+        # Set job name to first header if FASTA text input (random BioLib file) detected
+        if re.match('^input_[A-Za-z0-9]+.*', path_to_fasta):
+            first_id = next(SeqUtil.parse_fasta(path_to_fasta)).id
+            job_name = first_id.replace(' ', '_')[:60]
+
+        else:
+            job_name = file_path_to_stem(path_to_fasta)
+
+        logging.debug(f"Setting job name to '{job_name}' from {path_to_fasta}")
+
+        Runtime.set_result_name_prefix(job_name)
+
     @staticmethod
     def create_result_note(note: str) -> None:
         job_id = Runtime.get_job_id()

biolib/jobs/job.py

@@ -210,11 +210,14 @@ class Job:
         http_response = HttpClient.request(url=job_storage_input.get_remote_url())
         module_input_serialized = http_response.content
 
+        original_requested_machine = (
+            self._job_dict['requested_machine'] if self._job_dict['requested_machine'] else None
+        )
         job = self._start_job_in_cloud(
             app_uri=app_response['app_uri'],
             app_version_uuid=app_response['app_version']['public_id'],
             module_input_serialized=module_input_serialized,
-            machine=machine,
+            machine=machine if machine else original_requested_machine,
         )
         if blocking:
             job.stream_logs()

biolib/jobs/types.py

@@ -29,6 +29,7 @@ class JobDict(TypedDict):
     auth_token: str
     created_at: str
     ended_at: Optional[str]
+    requested_machine: str
     runtime_seconds: int
     main_result: Result
     started_at: str

{pybiolib-1.2.144.dev1.dist-info → pybiolib-1.2.158.dev1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.2.144.dev1
+Version: 1.2.158.dev1
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.2.144.dev1.dist-info → pybiolib-1.2.158.dev1.dist-info}/RECORD

@@ -26,7 +26,7 @@ biolib/_internal/types/resource_version.py,sha256=sLxViYXloDDUhTDFgjegiQCj097OM1
 biolib/_internal/types/typing.py,sha256=D4EKKEe7kDx0K6lJi-H_XLtk-8w6nu2fdqn9bvzI-Xo,288
 biolib/_internal/utils/__init__.py,sha256=p5vsIFyu-zYqBgdSMfwW9NC_jk7rXvvCbV4Bzd3As7c,630
 biolib/_internal/utils/multinode.py,sha256=zWrQhcVK5u_xdWX2oIM-D_2fINqNPlqF_h71fu4K8LY,8279
-biolib/_runtime/runtime.py,sha256=oVgTnDDJv9L4BUP1_sd0oAj4LLyyiPSQdhp7ixWARvw,2923
+biolib/_runtime/runtime.py,sha256=qV706-ZaBihrxSzD9ks62mbllJ3ruCoa6Ecf2zF7naA,3997
 biolib/api/__init__.py,sha256=mQ4u8FijqyLzjYMezMUUbbBGNB3iFmkNdjXnWPZ7Jlw,138
 biolib/api/client.py,sha256=FRpdH5aI187b_I_4HUNi680v4iOP65z5f2RcUo8D8MA,3559
 biolib/app/__init__.py,sha256=cdPtcfb_U-bxb9iSL4fCEq2rpD9OjkyY4W-Zw60B0LI,37
@@ -102,9 +102,9 @@ biolib/compute_node/webserver/worker_thread.py,sha256=GRRBUqXdMKvbjyLQhYlqGIbFKe
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=jIRixmQm3Gq9YdJ3I0-rE1vFukXqq6U4zXehFOJ1yZk,7614
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=ej-dxt1hMBQXzTfUZ2SLqIV8dtTbMSMn_q2rjIA7oN4,19903
+biolib/jobs/job.py,sha256=k9uksoA7BgSU-Mw5jHtuLHdTlg-G_d_89nVoPYcUnbg,20092
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
-biolib/jobs/types.py,sha256=qhadtH2KDC2WUOOqPiwke0YgtQY4FtuB71Stekq1k48,970
+biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/runtime/__init__.py,sha256=MlRepA11n2H-3plB5rzWyyHK2JmP6PiaP3i6x3vt0mg,506
 biolib/sdk/__init__.py,sha256=8uyOAKt8-Xo11jAWXCg14NkE1u0FkOBC07L3V7wGsCg,1960
 biolib/tables.py,sha256=acH7VjwAbadLo8P84FSnKEZxCTVsF5rEg9VPuxElNs8,872
@@ -119,8 +119,8 @@ 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=WJnU9vZdwY8RHXvzATyV80OXzyJ7w9EkG33Tna9Nr6A,5698
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.144.dev1.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.144.dev1.dist-info/METADATA,sha256=xXVO2tJLTCb1AV2U-KwCZBkGYelDWpZMNaIedHGM9Qg,1512
-pybiolib-1.2.144.dev1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.2.144.dev1.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.144.dev1.dist-info/RECORD,,
+pybiolib-1.2.158.dev1.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.158.dev1.dist-info/METADATA,sha256=7gYFVnp6YM8fLfHzg0S_XDeC6DxdTzeDX6dfWesenm0,1512
+pybiolib-1.2.158.dev1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.2.158.dev1.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.158.dev1.dist-info/RECORD,,