dcicutils 8.8.4.1b16__py3-none-any.whl → 8.8.4.1b18__py3-none-any.whl

dcicutils/file_utils.py

@@ -23,46 +23,59 @@ def search_for_file(file: str,
     first file which is found is returns (as a string), or None if none; if the single flag
     is False, then all matched files are returned in a list, or and empty list if none.
     """
-    if file and isinstance(file, (str, pathlib.PosixPath)):
-        if os.path.isabs(file):
-            if os.path.exists(file):
-                return file if single else [file]
-            return None if single else []
-        files_found = []
-        if not location:
-            location = ["."]
-        elif isinstance(location, (str, pathlib.PosixPath)):
-            location = [location]
-        elif not isinstance(location, list):
-            location = []
+    if not (file and isinstance(file, (str, pathlib.PosixPath))):
+        return None if single is True else []
+    if os.path.isabs(file):
+        if os.path.exists(file):
+            return file if single is True else [file]
+        return None if single is True else []
+    files_found = []
+    if not location:
+        location = ["."]
+    elif isinstance(location, (str, pathlib.PosixPath)):
+        location = [location]
+    elif not isinstance(location, list):
+        location = []
+    location_pruned = []
+    for directory in location:
+        if not isinstance(directory, str):
+            if not isinstance(directory, pathlib.PosixPath):
+                continue
+            directory = str(directory)
+        if not (directory := directory.strip()):
+            continue
+        if os.path.isfile(directory):
+            # Allow a file; assume its parent directory was intended.
+            if not (directory := os.path.dirname(directory)):
+                continue
+        location_pruned.append(directory)
+    location = location_pruned
+    for directory in location:
+        if os.path.exists(os.path.join(directory, file)):
+            file_found = os.path.abspath(os.path.normpath(os.path.join(directory, file)))
+            if single is True:
+                return file_found
+            if file_found not in files_found:
+                files_found.append(file_found)
+    if recursive is True:
         for directory in location:
             if not directory:
                 continue
-            if isinstance(directory, (str, pathlib.PosixPath)) and os.path.exists(os.path.join(directory, file)):
-                file_found = os.path.abspath(os.path.normpath(os.path.join(directory, file)))
-                if single:
-                    return file_found
-                if file_found not in files_found:
-                    files_found.append(file_found)
-        if recursive:
-            for directory in location:
-                if not directory:
-                    continue
-                if not directory.endswith("/**") and not file.startswith("**/"):
-                    path = f"{directory}/**/{file}"
-                else:
-                    path = f"{directory}/{file}"
-                files = glob.glob(path, recursive=recursive)
-                if files:
-                    for file_found in files:
-                        file_found = os.path.abspath(file_found)
-                        if single:
-                            return file_found
-                        if file_found not in files_found:
-                            files_found.append(file_found)
-        if files_found:
-            return files_found[0] if single else files_found
-        return None if single else []
+            if not directory.endswith("/**") and not file.startswith("**/"):
+                path = f"{directory}/**/{file}"
+            else:
+                path = f"{directory}/{file}"
+            files = glob.glob(path, recursive=True if recursive is True else False)
+            if files:
+                for file_found in files:
+                    file_found = os.path.abspath(file_found)
+                    if single is True:
+                        return file_found
+                    if file_found not in files_found:
+                        files_found.append(file_found)
+    if files_found:
+        return files_found[0] if single is True else files_found
+    return None if single is True else []
 
 
 def normalize_file_path(path: str, home_directory: bool = True) -> str:

dcicutils/http_utils.py

@@ -1,20 +1,31 @@
 from contextlib import contextmanager
 import requests
-from typing import Optional
+from typing import Callable, Optional
 from dcicutils.tmpfile_utils import temporary_file
 
 
 @contextmanager
-def download(url: str, suffix: Optional[str] = None, binary: bool = True) -> Optional[str]:
+def download(url: str, suffix: Optional[str] = None, binary: bool = True,
+             progress: Optional[Callable] = None) -> Optional[str]:
     """
     Context manager to ownload the given URL into a temporary file and yields the file
     path to it. An optional file suffix may be specified. Defaults to binary file mode;
     if this is not desired then pass False as the binary argument.
     """
+    if not callable(progress):
+        progress = None
     with temporary_file(suffix=suffix) as file:
         response = requests.get(url, stream=True)
+        if progress:
+            nbytes = 0
+            nbytes_total = None
+            if isinstance(content_length := response.headers.get("Content-Length"), str) and content_length.isdigit():
+                nbytes_total = int(content_length)
         with open(file, "wb" if binary is True else "w") as f:
             for chunk in response.iter_content(chunk_size=8192):
                 if chunk:
                     f.write(chunk)
+                if progress:
+                    nbytes += len(chunk)
+                    progress(nbytes, nbytes_total)
         yield file

{dcicutils-8.8.4.1b16.dist-info → dcicutils-8.8.4.1b18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.4.1b16
+Version: 8.8.4.1b18
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.8.4.1b16.dist-info → dcicutils-8.8.4.1b18.dist-info}/RECORD

@@ -28,10 +28,10 @@ dcicutils/es_utils.py,sha256=ZksLh5ei7kRUfiFltk8sd2ZSfh15twbstrMzBr8HNw4,7541
 dcicutils/exceptions.py,sha256=4giQGtpak-omQv7BP6Ckeu91XK5fnDosC8gfdmN_ccA,9931
 dcicutils/ff_mocks.py,sha256=6RKS4eUiu_Wl8yP_8V0CaV75w4ZdWxdCuL1CVlnMrek,36918
 dcicutils/ff_utils.py,sha256=oIhuZPnGtfwj6bWyCc1u23JbMB_6InPp01ZqUOljd8M,73123
-dcicutils/file_utils.py,sha256=msxA3fFTtK09Qc_I3-r9Y5Pp5WVJRPPpLlFYv3Rju-E,8697
+dcicutils/file_utils.py,sha256=GI3DfD11iM4Z76QbZftIJ1e6tWATxFtZ8as-vrlHTps,9139
 dcicutils/function_cache_decorator.py,sha256=XMyiEGODVr2WoAQ68vcoX_9_Xb9p8pZXdXl7keU8i2g,10026
 dcicutils/glacier_utils.py,sha256=Q4CVXsZCbP-SoZIsZ5NMcawDfelOLzbQnIlQn-GdlTo,34149
-dcicutils/http_utils.py,sha256=RB0x9hRMZM9Xd1x00c5J0iUzUdYzIQR0XKFiQ94HWO0,807
+dcicutils/http_utils.py,sha256=Je5ErNjR5e6lfSXGRncK_lcR_-zP38PIpmHjApy9Wi4,1289
 dcicutils/jh_utils.py,sha256=Gpsxb9XEzggF_-Eq3ukjKvTnuyb9V1SCSUXkXsES4Kg,11502
 dcicutils/kibana/dashboards.json,sha256=wHMB_mpJ8OaYhRRgvpZuihaB2lmSF64ADt_8hkBWgQg,16225
 dcicutils/kibana/readme.md,sha256=3KmHF9FH6A6xwYsNxRFLw27q0XzHYnjZOlYUnn3VkQQ,2164
@@ -73,8 +73,8 @@ dcicutils/trace_utils.py,sha256=g8kwV4ebEy5kXW6oOrEAUsurBcCROvwtZqz9fczsGRE,1769
 dcicutils/validation_utils.py,sha256=cMZIU2cY98FYtzK52z5WUYck7urH6JcqOuz9jkXpqzg,14797
 dcicutils/variant_utils.py,sha256=2H9azNx3xAj-MySg-uZ2SFqbWs4kZvf61JnK6b-h4Qw,4343
 dcicutils/zip_utils.py,sha256=_Y9EmL3D2dUZhxucxHvrtmmlbZmK4FpSsHEb7rGSJLU,3265
-dcicutils-8.8.4.1b16.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.8.4.1b16.dist-info/METADATA,sha256=7R_Eatzjy4Ez8_JufgAKLIQ_O6z0fVvjqHzLEwfE9O0,3440
-dcicutils-8.8.4.1b16.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.8.4.1b16.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
-dcicutils-8.8.4.1b16.dist-info/RECORD,,
+dcicutils-8.8.4.1b18.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.8.4.1b18.dist-info/METADATA,sha256=YbKpFyKttkQQ6Exbw6SfcOkW76dDpxqlJ2DhyBHzTxM,3440
+dcicutils-8.8.4.1b18.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.8.4.1b18.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
+dcicutils-8.8.4.1b18.dist-info/RECORD,,