pybiolib 1.1.1629__tar.gz → 1.1.1641__tar.gz

{pybiolib-1.1.1629 → pybiolib-1.1.1641}/PKG-INFO

@@ -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 → pybiolib-1.1.1641}/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:

{pybiolib-1.1.1629 → pybiolib-1.1.1641}/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 → pybiolib-1.1.1641}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pybiolib"
-version = "1.1.1629"
+version = "1.1.1641"
 description = "BioLib Python Client"
 readme = "README.md"
 license = "MIT"