dcicutils 8.8.4__py3-none-any.whl → 8.8.4.1b2__py3-none-any.whl

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/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/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/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.dist-info → dcicutils-8.8.4.1b2.dist-info}/METADATA

@@ -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.dist-info → dcicutils-8.8.4.1b2.dist-info}/RECORD

@@ -27,10 +27,11 @@ dcicutils/env_utils_legacy.py,sha256=J81OAtJHN69o1beHO6q1j7_J6TeblSjnAHlS8VA5KSM
 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=Yf-fET5gdpjrH0gikpOCIJdY2Dv3obzUpR31ur816mU,72972
+dcicutils/ff_utils.py,sha256=oIhuZPnGtfwj6bWyCc1u23JbMB_6InPp01ZqUOljd8M,73123
 dcicutils/file_utils.py,sha256=098rXvLeIh8n69EGW7DpOS227ef3BPgwhRAktoU6mhE,2663
 dcicutils/function_cache_decorator.py,sha256=XMyiEGODVr2WoAQ68vcoX_9_Xb9p8pZXdXl7keU8i2g,10026
 dcicutils/glacier_utils.py,sha256=Q4CVXsZCbP-SoZIsZ5NMcawDfelOLzbQnIlQn-GdlTo,34149
+dcicutils/http_utils.py,sha256=UKIsP-e8NOZN_4ScLDoFA4Bd1ifYBLTl6RrwvRfuAPY,549
 dcicutils/jh_utils.py,sha256=Gpsxb9XEzggF_-Eq3ukjKvTnuyb9V1SCSUXkXsES4Kg,11502
 dcicutils/kibana/dashboards.json,sha256=wHMB_mpJ8OaYhRRgvpZuihaB2lmSF64ADt_8hkBWgQg,16225
 dcicutils/kibana/readme.md,sha256=3KmHF9FH6A6xwYsNxRFLw27q0XzHYnjZOlYUnn3VkQQ,2164
@@ -43,7 +44,7 @@ dcicutils/license_policies/park-lab-gpl-pipeline.jsonc,sha256=vLZkwm3Js-kjV44nug
 dcicutils/license_policies/park-lab-pipeline.jsonc,sha256=9qlY0ASy3iUMQlr3gorVcXrSfRHnVGbLhkS427UaRy4,283
 dcicutils/license_utils.py,sha256=d1cq6iwv5Ju-VjdoINi6q7CPNNL7Oz6rcJdLMY38RX0,46978
 dcicutils/log_utils.py,sha256=7pWMc6vyrorUZQf-V-M3YC6zrPgNhuV_fzm9xqTPph0,10883
-dcicutils/misc_utils.py,sha256=YH_TTmv6ABWeMERwVvA2-rIfdS-CoPYLXJru9TvWxgM,104610
+dcicutils/misc_utils.py,sha256=hdL7FP2fMTX6OuJ9SXyAS4BLvrNUBLk8XOQHRw_EeiI,105041
 dcicutils/obfuscation_utils.py,sha256=fo2jOmDRC6xWpYX49u80bVNisqRRoPskFNX3ymFAmjw,5963
 dcicutils/opensearch_utils.py,sha256=V2exmFYW8Xl2_pGFixF4I2Cc549Opwe4PhFi5twC0M8,1017
 dcicutils/portal_object_utils.py,sha256=gDXRgPsRvqCFwbC8WatsuflAxNiigOnqr0Hi93k3AgE,15422
@@ -71,9 +72,9 @@ dcicutils/tmpfile_utils.py,sha256=n95XF8dZVbQRSXBZTGToXXfSs3JUVRyN6c3ZZ0nhAWI,14
 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=rnjNv_k6L9jT2SjDSgVXp4BEJYLtz9XN6Cl2Fy-tqnM,2027
-dcicutils-8.8.4.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.8.4.dist-info/METADATA,sha256=fMdiyQonxO9h426d8jDY59u47FAfvXcNrwRXW0GmsIY,3352
-dcicutils-8.8.4.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.8.4.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
-dcicutils-8.8.4.dist-info/RECORD,,
+dcicutils/zip_utils.py,sha256=dEnUZ1GHfJHPmqXBIqYRorsClSeUTPADoBMxp9TWacI,2994
+dcicutils-8.8.4.1b2.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.8.4.1b2.dist-info/METADATA,sha256=IXQBCwnsqr2r6XPr-LJ2LOZ4zcYjklc0D_DILN7dVeo,3396
+dcicutils-8.8.4.1b2.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.8.4.1b2.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
+dcicutils-8.8.4.1b2.dist-info/RECORD,,