pybiolib 1.2.659__py3-none-any.whl → 1.2.678__py3-none-any.whl

biolib/_internal/tree_utils.py

@@ -0,0 +1,106 @@
+"""Utilities for displaying file trees and formatting file sizes."""
+
+from typing import Any, Dict, List, Optional, Union
+
+from biolib.biolib_binary_format.utils import LazyLoadedFile
+
+
+def format_size(size_bytes: int) -> str:
+    """Convert bytes to human-readable format (e.g., 2.5KB).
+
+    Args:
+        size_bytes: File size in bytes
+
+    Returns:
+        Human-readable string representation of the file size
+    """
+    if size_bytes < 1024:
+        return f'{size_bytes}B'
+    elif size_bytes < 1024 * 1024:
+        return f'{size_bytes/1024:.1f}KB'
+    elif size_bytes < 1024 * 1024 * 1024:
+        return f'{size_bytes/(1024*1024):.1f}MB'
+    else:
+        return f'{size_bytes/(1024*1024*1024):.1f}GB'
+
+
+def build_tree_str(
+    data: Dict[str, Any],
+    prefix: str = '',
+    tree_lines: Optional[List[str]] = None,
+    blue: str = '\033[34m',
+    white: str = '\033[90m',  # Changed from white (37m) to dark gray (90m) for better visibility on light backgrounds
+    reset: str = '\033[0m',
+) -> List[str]:
+    """Build a string representation of a file tree with color-coded directories and files.
+
+    Args:
+        data: Hierarchical tree structure of directories and files
+        prefix: Line prefix for indentation and tree structure characters
+        tree_lines: List to accumulate tree lines
+        blue: ANSI color code for directories
+        white: ANSI color code for files (defaults to dark gray for visibility on light backgrounds)
+        reset: ANSI color code to reset color
+
+    Returns:
+        List of tree lines for display
+    """
+    if tree_lines is None:
+        tree_lines = []
+
+    # Get sorted items, keeping directories first
+    items = sorted([(k, v) for k, v in data.items() if k != '__files__'])
+    files_list = sorted(data.get('__files__', []), key=lambda f: f['name'])
+
+    # Add directories
+    for i, (key, value) in enumerate(items):
+        is_last_dir = i == len(items) - 1 and not files_list
+
+        if is_last_dir:
+            tree_lines.append(f'{prefix}└── {blue}{key}{reset}')
+            build_tree_str(value, prefix + '    ', tree_lines, blue, white, reset)
+        else:
+            tree_lines.append(f'{prefix}├── {blue}{key}{reset}')
+            build_tree_str(value, prefix + '│   ', tree_lines, blue, white, reset)
+
+    # Add files with their sizes
+    for i, file in enumerate(files_list):
+        is_last = i == len(files_list) - 1
+        size_str = format_size(file['size'])
+        file_name = file['name']
+
+        if is_last:
+            tree_lines.append(f'{prefix}└── {white}{file_name} ({size_str}){reset}')
+        else:
+            tree_lines.append(f'{prefix}├── {white}{file_name} ({size_str}){reset}')
+
+    return tree_lines
+
+
+def build_tree_from_files(files: List[LazyLoadedFile]) -> Dict[str, Union[Dict[str, Any], List[Dict[str, Any]]]]:
+    """Build a hierarchical tree structure from a list of files.
+
+    Args:
+        files: List of files to organize into a tree
+
+    Returns:
+        Hierarchical tree structure of directories and files
+    """
+    tree: Dict[str, Union[Dict[str, Any], List[Dict[str, Any]]]] = {}
+    for file in files:
+        parts = file.path.lstrip('/').split('/')
+        current: Dict[str, Union[Dict[str, Any], List[Dict[str, Any]]]] = tree
+        for i, part in enumerate(parts):
+            if i == len(parts) - 1:  # This is a file
+                if '__files__' not in current:
+                    current['__files__'] = []
+                files_list = current['__files__']
+                assert isinstance(files_list, list)
+                files_list.append({'name': part, 'size': file.length})
+            else:  # This is a directory
+                if part not in current:
+                    current[part] = {}
+                dir_dict = current[part]
+                assert isinstance(dir_dict, dict)
+                current = dir_dict
+    return tree

biolib/jobs/job.py

@@ -9,6 +9,7 @@ from urllib.parse import urlparse
 import biolib.api.client
 from biolib import utils
 from biolib._internal.http_client import HttpClient
+from biolib._internal.tree_utils import build_tree_from_files, build_tree_str
 from biolib._internal.utils import open_browser_window_from_notebook
 from biolib.api.client import ApiClient
 from biolib.biolib_api_client import BiolibApiClient, CreatedJobDict
@@ -56,7 +57,48 @@ class Job:
         return f"Job for {self._job_dict['app_uri']} created at {self._job_dict['created_at']} ({self._uuid})"
 
     def __repr__(self):
-        return f'Job: {self._uuid}'
+        # Get job status and shareable link
+        status = self.get_status()
+        shareable_link = self.get_shareable_link()
+
+        # ANSI color codes for terminal output
+        blue = '\033[34m'
+        white = '\033[37m'
+        reset = '\033[0m'
+
+        # Start with the header section
+        output_lines = [
+            '--- BioLib Result ---',
+            f'ID: {self._uuid}',
+            f'Status: {status}',
+            f'Link: {shareable_link}',
+        ]
+
+        # Only show output files if the job is not pending
+        if not self.is_pending():
+            output_lines.append('Output Files:')
+
+            try:
+                # Get files from the job
+                files = self.list_output_files()
+
+                # If no files, indicate that
+                if not files:
+                    output_lines.append('No output files')
+                    return '\n'.join(output_lines)
+
+                # If more than 25 files, show simplified message
+                if len(files) > 25:
+                    output_lines.append(f'{len(files)} output files in result.')
+                    return '\n'.join(output_lines)
+
+                # Build the tree representation
+                tree_data = build_tree_from_files(files)
+                output_lines.extend(build_tree_str(tree_data, blue=blue, white=white, reset=reset))
+            except Exception:
+                output_lines.append('Error accessing output files')
+
+        return '\n'.join(output_lines)
 
     @property
     def id(self) -> str:  # pylint: disable=invalid-name
@@ -128,6 +170,21 @@ class Job:
         self,
         path_filter: Optional[PathFilter] = None,
     ) -> List[LazyLoadedFile]:
+        """List output files from the job.
+
+        Args:
+            path_filter (PathFilter, optional): Filter to apply to the output files.
+                Can be a string glob pattern or a callable that takes a path string and returns a boolean.
+
+        Returns:
+            List[LazyLoadedFile]: List of output files.
+
+        Example::
+            >>> job = biolib.get_job("job_id")
+            >>> output_files = job.list_output_files()
+            >>> # Filter files with a glob pattern
+            >>> output_files = job.list_output_files("*.pdb")
+        """
         return self.result.list_output_files(path_filter=path_filter)
 
     def get_output_file(self, filename: str) -> LazyLoadedFile:

{pybiolib-1.2.659.dist-info → pybiolib-1.2.678.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: pybiolib
-Version: 1.2.659
+Version: 1.2.678
 Summary: BioLib Python Client
 License: MIT
 Keywords: biolib

{pybiolib-1.2.659.dist-info → pybiolib-1.2.678.dist-info}/RECORD

@@ -19,6 +19,7 @@ biolib/_internal/llm_instructions/.github/prompts/biolib_run_apps.prompt.md,sha2
 biolib/_internal/llm_instructions/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/_internal/push_application.py,sha256=Ffj3iZ0nma4KHTB-PKCeFvhCHHhAEhgKClxnfBUpL8U,12296
 biolib/_internal/runtime.py,sha256=BiHl4klUHr36MCpqKaUso4idHeBZfPAahLYRQrabFqA,486
+biolib/_internal/tree_utils.py,sha256=_Q_6_NDtIiROcefymqxEVddjqti6Mt3OZ4U0GcDW61s,3904
 biolib/_internal/types/__init__.py,sha256=xLgOQJFh3GRtiqIJq7MaqHReZx4pp34_zcaFQ_JjuJ4,198
 biolib/_internal/types/app.py,sha256=Mz2QGD_jESX-K9JYnLWPo4YA__Q_1FQQTk9pvidCohU,118
 biolib/_internal/types/data_record.py,sha256=9r_vdhVs60YTnzU4XQFXfDrfS2P2MqD3BH2xa7lk6ck,852
@@ -107,7 +108,7 @@ biolib/compute_node/webserver/worker_thread.py,sha256=7uD9yQPhePYvP2HCJ27EeZ_h6p
 biolib/experiments/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 biolib/experiments/experiment.py,sha256=pBtnOHz0kKoFxlIGf08o8ZCEOze-CljwfOsTdhvCTCk,8646
 biolib/jobs/__init__.py,sha256=aIb2H2DHjQbM2Bs-dysFijhwFcL58Blp0Co0gimED3w,32
-biolib/jobs/job.py,sha256=rcQPLrUsVHdzZ0g_T9f3m_mmVF0m-aYi_fKYTbQATaA,24174
+biolib/jobs/job.py,sha256=nHSYUIUcvujfh6Q85j1qLGIWzXKwp4kEou8ywhngJlQ,26276
 biolib/jobs/job_result.py,sha256=rALHiKYNaC9lHi_JJqBob1RubzNLwG9Z386kwRJjd2M,5885
 biolib/jobs/types.py,sha256=ezvaoTANsWazK6PmfpYcqezdfjP7MNBEBfqIZGoZhz8,997
 biolib/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -125,8 +126,8 @@ 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=Ozk0blGtPur_D9MwShD02r_mphyQmgZkx-lOHOwnlIM,6730
 biolib/utils/zip/remote_zip.py,sha256=0wErYlxir5921agfFeV1xVjf29l9VNgGQvNlWOlj2Yc,23232
-pybiolib-1.2.659.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
-pybiolib-1.2.659.dist-info/METADATA,sha256=qpaLR_QUpfGpkRX0F9kNFxh5_I5GGlh1eLnIfzopGs4,1570
-pybiolib-1.2.659.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
-pybiolib-1.2.659.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
-pybiolib-1.2.659.dist-info/RECORD,,
+pybiolib-1.2.678.dist-info/LICENSE,sha256=F2h7gf8i0agDIeWoBPXDMYScvQOz02pAWkKhTGOHaaw,1067
+pybiolib-1.2.678.dist-info/METADATA,sha256=x4HkSXSKyAR_YIOCHMl7SfrdBptlfAuj2XLTsKjW_cw,1570
+pybiolib-1.2.678.dist-info/WHEEL,sha256=fGIA9gx4Qxk2KDKeNJCbOEwSrmLtjWCwzBz351GyrPQ,88
+pybiolib-1.2.678.dist-info/entry_points.txt,sha256=p6DyaP_2kctxegTX23WBznnrDi4mz6gx04O5uKtRDXg,42
+pybiolib-1.2.678.dist-info/RECORD,,