pybiolib 1.2.142__tar.gz → 1.2.152.dev1__tar.gz

{pybiolib-1.2.142 → pybiolib-1.2.152.dev1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.2.142
+Version: 1.2.152.dev1
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.2.142 → pybiolib-1.2.152.dev1}/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()

{pybiolib-1.2.142 → pybiolib-1.2.152.dev1}/biolib/compute_node/job_worker/executors/docker_executor.py

@@ -359,7 +359,7 @@ class DockerExecutor:
 
             if utils.IS_RUNNING_IN_CLOUD:
                 cloud_job = self._options['cloud_job']
-                create_container_args['mem_limit'] = f'{cloud_job["reserved_memory_in_bytes"]}b'
+                create_container_args['mem_limit'] = f'{cloud_job["reserved_memory_in_bytes"] - 500_000_000}b'
                 create_container_args['nano_cpus'] = cloud_job['reserved_cpu_in_nano_shares']
                 create_container_args['pids_limit'] = 10_000
 

{pybiolib-1.2.142 → pybiolib-1.2.152.dev1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.2.142"
+version = "1.2.152.dev1"
 description = "BioLib Python Client"
 readme = "PYPI_README.md"
 license = "MIT"