pybiolib 1.2.142__py3-none-any.whl → 1.2.152.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/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.dist-info → pybiolib-1.2.152.dev1.dist-info}/METADATA

@@ -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.dist-info → pybiolib-1.2.152.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
@@ -77,7 +77,7 @@ 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=LcYc4x4-vkmRM1FN1SNj7xRj4qZUNVjQWtgbYMFg3JU,28029
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=qp8yc1BOkLNpSHbU04H314KVK_c_AjqVsuDrDlMTHbg,28043
 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
@@ -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-1.2.142.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.142.dist-info/METADATA,sha256=PvwsBYAZig3L7Re_cMg6Sq3K-25M4aNMeSw6joKGg3Y,1507
-pybiolib-1.2.142.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-pybiolib-1.2.142.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.142.dist-info/RECORD,,
+pybiolib-1.2.152.dev1.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.152.dev1.dist-info/METADATA,sha256=Ngmm-Y2RC8rGaqRpWNWT_uJYz59jxm1_SNTUKa8Zn4M,1512
+pybiolib-1.2.152.dev1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+pybiolib-1.2.152.dev1.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.152.dev1.dist-info/RECORD,,