pybiolib 1.1.1629__py3-none-any.whl → 1.1.1641__py3-none-any.whl

biolib/compute_node/job_worker/executors/docker_executor.py

@@ -551,7 +551,7 @@ class DockerExecutor:
                 'Docker UpperDir not available. Falling back to container.get_archive() for file extraction'
             )
 
-        logger.debug(f'overlay_upper_dir_path={overlay_upper_dir_path}')
+        logger_no_user_data.debug(f'overlay_upper_dir_path={overlay_upper_dir_path}')
 
         files_and_empty_dirs: List[FileInContainer] = []
         for path in run_diff_paths:

biolib/utils/seq_util.py

@@ -1,4 +1,5 @@
-from biolib.typing_utils import List, Optional
+import re
+from biolib.typing_utils import List, Optional, Dict
 
 allowed_sequence_chars = set("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789-_.")
 def find_invalid_sequence_characters(sequence):
@@ -6,11 +7,24 @@ def find_invalid_sequence_characters(sequence):
     return invalid_chars
 
 class SeqUtilRecord:
-    def __init__(self, sequence: str, sequence_id: str, description: Optional['str']):
+    def __init__(self,
+                 sequence: str,
+                 sequence_id: str,
+                 description: Optional['str'],
+                 properties: Optional[Dict[str, str]] = None):
         self.sequence = sequence
         self.id = sequence_id  # pylint: disable=invalid-name
         self.description = description
 
+        if properties:
+            disallowed_pattern = re.compile(r"[=\[\]\n]")
+            for key, value in properties.items():
+                assert not bool(disallowed_pattern.search(key)), "Key cannot contain characters =[] and newline"
+                assert not bool(disallowed_pattern.search(value)), "Value cannot contain characters =[] and newline"
+            self.properties = properties
+        else:
+            self.properties = {}
+
     def __repr__(self) -> str:
         return f'{self.__class__.__name__} ({self.id})'
 
@@ -78,5 +92,8 @@ class SeqUtil:
         with open(file_name, mode='w') as file_handle:
             for record in records:
                 optional_description = f' {record.description}' if record.description else ''
+                if record.properties:
+                    for key, value in record.properties.items():
+                        optional_description += f' [{key}={value}]'
                 sequence = '\n'.join(record.sequence[i:i + 80] for i in range(0, len(record.sequence), 80))
                 file_handle.write(f'>{record.id}{optional_description}\n{sequence}\n')

{pybiolib-1.1.1629.dist-info → pybiolib-1.1.1641.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pybiolib
-Version: 1.1.1629
+Version: 1.1.1641
 Summary: BioLib Python Client
 Home-page: https://github.com/biolib
 License: MIT

{pybiolib-1.1.1629.dist-info → pybiolib-1.1.1641.dist-info}/RECORD

@@ -54,7 +54,7 @@ biolib/compute_node/job_worker/cache_state.py,sha256=N2AxvvgfizKx9P_ysM0GDCmueMU
 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=74wUy5piILgCY-eFu2LuEOWDqmuYkaijy-ZW83S6WKw,26335
+biolib/compute_node/job_worker/executors/docker_executor.py,sha256=vXL2Y7bemwjcICbq78m3K8DsNHkImYl1fgQhnWMYQOs,26348
 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
@@ -99,10 +99,10 @@ biolib/utils/__init__.py,sha256=RxXoO8sLfmv5UIdkYAX7p5K03UUIUzss_A5vtb8CLlw,6897
 biolib/utils/app_uri.py,sha256=hOFsTQfA7QbyQyg9ItGdD8VDWBJw0vYMqzLdSiJXmqQ,1857
 biolib/utils/cache_state.py,sha256=BFrZlV4XZIueIFzAFiPidX4hmwADKY5Y5ZuqlerF5l0,3060
 biolib/utils/multipart_uploader.py,sha256=PEorMsTNg5f72e3Y-KA3LrI-F6EAnsD9vENV-5EuiX0,9896
-biolib/utils/seq_util.py,sha256=hudZ7o1LI7xdpjb1OFKPBZvGVxjiqKez8zMwjtWT0TY,3269
+biolib/utils/seq_util.py,sha256=7EwBNJ0yFAfX1lTOwf5IpcbjdNZ8u0TeHf8gW9n28IA,4019
 biolib/utils/zip/remote_zip.py,sha256=NCdUnVbGCv7SfXCI-yVU-is_OnyWmLAnVpIdSvo-W4k,23500
-pybiolib-1.1.1629.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.1.1629.dist-info/METADATA,sha256=grvWM24XHQjGcGXpjHv79ba0vY8PzvyTce4CUjkQ3wk,1543
-pybiolib-1.1.1629.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
-pybiolib-1.1.1629.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.1.1629.dist-info/RECORD,,
+pybiolib-1.1.1641.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.1.1641.dist-info/METADATA,sha256=QAbbPvjHwCp16EXECXjNiVJalta7-_lvrSjrFuF2COw,1543
+pybiolib-1.1.1641.dist-info/WHEEL,sha256=FMvqSimYX_P7y0a7UY-_Mc83r5zkBZsCYPm7Lr0Bsq4,88
+pybiolib-1.1.1641.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.1.1641.dist-info/RECORD,,