dcicutils 8.8.4__tar.gz → 8.8.4.1b2__tar.gz

{dcicutils-8.8.4 → dcicutils-8.8.4.1b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.8.4
+Version: 8.8.4.1b2
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT
@@ -24,6 +24,7 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Topic :: Database :: Database Engines/Servers
 Requires-Dist: PyJWT (>=2.6.0,<3.0.0)
 Requires-Dist: PyYAML (>=6.0.1,<7.0.0)
+Requires-Dist: appdirs (>=1.4.4,<2.0.0)
 Requires-Dist: aws-requests-auth (>=0.4.2,<1)
 Requires-Dist: boto3 (>=1.28.57,<2.0.0)
 Requires-Dist: botocore (>=1.31.57,<2.0.0)

{dcicutils-8.8.4 → dcicutils-8.8.4.1b2}/dcicutils/ff_utils.py

@@ -895,9 +895,12 @@ def _get_es_metadata(uuids, es_client, filters, sources, chunk_size, auth):
     used to create the generator.
     Should NOT be used directly
     """
+    def get_es_host_local() -> Optional[str]:
+        return os.environ.get("ES_HOST_LOCAL", None)
     health = get_health_page(key=auth)
     if es_client is None:
-        es_url = health['elasticsearch']
+        if not (es_url := get_es_host_local()):
+            es_url = health['elasticsearch']
         es_client = es_utils.create_es_client(es_url, use_aws_auth=True)
     namespace_star = health.get('namespace', '') + '*'
     # match all given uuids to _id fields

dcicutils-8.8.4.1b2/dcicutils/http_utils.py

@@ -0,0 +1,15 @@
+from contextlib import contextmanager
+import requests
+from typing import Optional
+from dcicutils.tmpfile_utils import temporary_file
+
+
+@contextmanager
+def download(url: str, suffix: Optional[str] = None, binary: bool = True) -> Optional[str]:
+    with temporary_file(suffix=suffix) as file:
+        response = requests.get(url, stream=True)
+        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)
+        yield file

{dcicutils-8.8.4 → dcicutils-8.8.4.1b2}/dcicutils/misc_utils.py

@@ -3,6 +3,7 @@ This file contains functions that might be generally useful.
 """
 
 from collections import namedtuple
+import appdirs
 import contextlib
 import datetime
 import functools
@@ -2670,3 +2671,14 @@ class JsonLinesReader:
                 yield line
             else:
                 raise Exception(f"If the first line is not a list, all lines must be dictionaries: {line!r}")
+
+
+def get_app_specific_directory() -> str:
+    """
+    Returns the standard system application specific directory:
+    - On MacOS this directory: is: ~/Library/Application Support
+    - On Linux this directory is: ~/.local/share
+    - On Windows this directory is: %USERPROFILE%\AppData\Local  # noqa
+    N.B. This is has been tested on MacOS and Linux but not on Windows.
+    """
+    return appdirs.user_data_dir()

{dcicutils-8.8.4 → dcicutils-8.8.4.1b2}/dcicutils/zip_utils.py

@@ -2,7 +2,9 @@ from contextlib import contextmanager
 from dcicutils.tmpfile_utils import temporary_directory, temporary_file
 import gzip
 import os
+import shutil
 import tarfile
+import tempfile
 from typing import List, Optional
 import zipfile
 
@@ -45,3 +47,23 @@ def unpack_gz_file_to_temporary_file(file: str, suffix: Optional[str] = None) ->
                     outputf.write(inputf.read())
                     outputf.close()
                     yield tmp_file_name
+
+
+def extract_file_from_zip(zip_file: str, file_to_extract: str,
+                          destination_file: str, raise_exception: bool = True) -> bool:
+    try:
+        if not (destination_directory := os.path.dirname(destination_file)):
+            destination_directory = os.getcwd()
+            destination_file = os.path.join(destination_directory, destination_file)
+        with tempfile.TemporaryDirectory() as tmp_directory_name:
+            with zipfile.ZipFile(zip_file, "r") as zipf:
+                if file_to_extract not in zipf.namelist():
+                    return False
+                zipf.extract(file_to_extract, path=tmp_directory_name)
+                os.makedirs(destination_directory, exist_ok=True)
+                shutil.move(os.path.join(tmp_directory_name, file_to_extract), destination_file)
+            return True
+    except Exception as e:
+        if raise_exception:
+            raise e
+    return False

{dcicutils-8.8.4 → dcicutils-8.8.4.1b2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4"
+version = "8.8.4.1b2"  # TODO: To become 8.8.5
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -43,6 +43,7 @@ botocore = "^1.31.57"
 # The DCIC portals (cgap-portal and fourfront) are very particular about which ElasticSearch version.
 # This value is intentionally pinned and must not be changed casually.
 elasticsearch = "7.13.4"
+appdirs = "^1.4.4"
 aws-requests-auth = ">=0.4.2,<1"
 chardet = "^5.2.0"
 docker = "^4.4.4"