From 640043af4bc3734a0304d444f79276cc2d4c9637 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 23 Apr 2024 17:40:43 -0400
Subject: [PATCH 01/46] Added check for ES_HOST_LOCAL environment variable in
 ff_utils.get_es_metadata.

---
 CHANGELOG.rst         | 7 +++++++
 dcicutils/ff_utils.py | 5 ++++-
 pyproject.toml        | 2 +-
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 1054c4c08..5d65fd425 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -7,6 +7,13 @@ Change Log
 ----------
 
 
+8.8.5
+=====
+* Added check for ES_HOST_LOCAL environment variable in ff_utils.get_es_metadata;
+  for running Foursight checks locally (with local ssh tunnel to ES proxy);
+  came up in foursight/checks/audit_checks (2024-04-23).
+
+
 8.8.4
 =====
 * Minor fix in structured_data to not try to resolve empty refs in norefs mode;
diff --git a/dcicutils/ff_utils.py b/dcicutils/ff_utils.py
index e2c6ac089..442a9642e 100644
--- a/dcicutils/ff_utils.py
+++ b/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
diff --git a/pyproject.toml b/pyproject.toml
index e34d933d0..abc17f6fe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4"
+version = "8.8.4.1b1"  # 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"

From e8971e25eaf6d41692b16b0b51140604e00cfc76 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 23 Apr 2024 17:55:37 -0400
Subject: [PATCH 02/46] Added extract_file_from_zip to zip_utils. Added
 http_utils with download function.

---
 CHANGELOG.rst             |  2 ++
 dcicutils/http_utils.py   | 15 +++++++++++++++
 dcicutils/zip_utils.py    | 22 ++++++++++++++++++++++
 docs/source/dcicutils.rst |  7 +++++++
 4 files changed, 46 insertions(+)
 create mode 100644 dcicutils/http_utils.py

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 5d65fd425..267918f87 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -12,6 +12,8 @@ Change Log
 * Added check for ES_HOST_LOCAL environment variable in ff_utils.get_es_metadata;
   for running Foursight checks locally (with local ssh tunnel to ES proxy);
   came up in foursight/checks/audit_checks (2024-04-23).
+* Added extract_file_from_zip to zip_utils.
+* Added http_utils with download function.
 
 
 8.8.4
diff --git a/dcicutils/http_utils.py b/dcicutils/http_utils.py
new file mode 100644
index 000000000..a080dec06
--- /dev/null
+++ b/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
diff --git a/dcicutils/zip_utils.py b/dcicutils/zip_utils.py
index 8a65f8abe..a262ce549 100644
--- a/dcicutils/zip_utils.py
+++ b/dcicutils/zip_utils.py
@@ -2,7 +2,9 @@
 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
diff --git a/docs/source/dcicutils.rst b/docs/source/dcicutils.rst
index 6241dd41c..b33b8a2b5 100644
--- a/docs/source/dcicutils.rst
+++ b/docs/source/dcicutils.rst
@@ -225,6 +225,13 @@ glacier_utils
    :members:
 
 
+http_utils
+^^^^^^^^^^^
+
+.. automodule:: dcicutils.http_utils
+  :members:
+
+
 lang_utils
 ^^^^^^^^^^
 

From 4c973b8409d543ca0dabaefae451c6d82106be34 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 23 Apr 2024 18:02:45 -0400
Subject: [PATCH 03/46] added get_app_specific_directory to misc_utils

---
 CHANGELOG.rst           |  1 +
 dcicutils/misc_utils.py | 12 ++++++++++++
 2 files changed, 13 insertions(+)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 267918f87..3ec0d5317 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -14,6 +14,7 @@ Change Log
   came up in foursight/checks/audit_checks (2024-04-23).
 * Added extract_file_from_zip to zip_utils.
 * Added http_utils with download function.
+* Added get_app_specific_directory to misc_utils.
 
 
 8.8.4
diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index a5979fb36..6814dddd2 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -3,6 +3,7 @@
 """
 
 from collections import namedtuple
+import appdirs
 import contextlib
 import datetime
 import functools
@@ -2670,3 +2671,14 @@ def __iter__(self):
                 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()

From b6bf2db94fb883734b43afa876c311eb0562478a Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 23 Apr 2024 18:05:32 -0400
Subject: [PATCH 04/46] added appdirs dependency

---
 poetry.lock    | 13 ++++++++++++-
 pyproject.toml |  3 ++-
 2 files changed, 14 insertions(+), 2 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index dcb11a4bb..51d31667f 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,5 +1,16 @@
 # This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
 
+[[package]]
+name = "appdirs"
+version = "1.4.4"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+optional = false
+python-versions = "*"
+files = [
+    {file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
+    {file = "appdirs-1.4.4.tar.gz", hash = "sha256:7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41"},
+]
+
 [[package]]
 name = "async-timeout"
 version = "4.0.2"
@@ -2102,4 +2113,4 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.12"
-content-hash = "3be12a7e28700d3e0b98a00738192dbc8070e3c37279cccd179618ff7dc23757"
+content-hash = "87d855b9552dbd71f3afc072689b548b0eb7b540a4decee3a6f6993312a84fac"
diff --git a/pyproject.toml b/pyproject.toml
index abc17f6fe..90f6b6424 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b1"  # TODO: To become 8.8.5
+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"

From 9453875da29d7a0418af06829c3235070840955e Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 24 Apr 2024 09:40:58 -0400
Subject: [PATCH 05/46] Added normalize_file_path to file_utils.

---
 CHANGELOG.rst           |  1 +
 dcicutils/file_utils.py | 14 ++++++++++++++
 pyproject.toml          |  2 +-
 3 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 3ec0d5317..b3fdc0582 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -15,6 +15,7 @@ Change Log
 * Added extract_file_from_zip to zip_utils.
 * Added http_utils with download function.
 * Added get_app_specific_directory to misc_utils.
+* Added normalize_file_path to file_utils.
 
 
 8.8.4
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 9ad6c6dc7..6bb4971ae 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -56,3 +56,17 @@ def search_for_file(file: str,
         if files_found:
             return files_found[0] if single else files_found
         return None if single else []
+
+
+def normalize_file_path(path: str, including_home_directory: bool = False) -> str:
+    if not isinstance(path, str) or not path:
+        path = os.getcwd()
+    path = os.path.normpath(path)
+    home_directory = os.path.expanduser("~")
+    if path.startswith("~"):
+        path = os.path.join(home_directory, path[2 if path.startswith("~/") else 1:])
+    path = os.path.abspath(path)
+    if including_home_directory and (os.name == "posix"):
+        if path.startswith(home_directory) and path != home_directory:
+            path = "~/" + pathlib.Path(path).relative_to(home_directory).as_posix()
+    return path
diff --git a/pyproject.toml b/pyproject.toml
index 90f6b6424..9f64ef1d9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b2"  # TODO: To become 8.8.5
+version = "8.8.4.1b3"  # 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"

From dc0ac44454cb6dd3e61961bd0f246b6e1d717fad Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 24 Apr 2024 10:30:00 -0400
Subject: [PATCH 06/46] minor updates

---
 CHANGELOG.rst           |  3 ++-
 dcicutils/file_utils.py | 14 ++++++++++----
 dcicutils/http_utils.py |  5 +++++
 dcicutils/misc_utils.py | 16 ++++++++++++++++
 pyproject.toml          |  2 +-
 5 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index b3fdc0582..6fc32f569 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -9,12 +9,13 @@ Change Log
 
 8.8.5
 =====
+* 2024-04-23/dmichaels
 * Added check for ES_HOST_LOCAL environment variable in ff_utils.get_es_metadata;
   for running Foursight checks locally (with local ssh tunnel to ES proxy);
   came up in foursight/checks/audit_checks (2024-04-23).
 * Added extract_file_from_zip to zip_utils.
 * Added http_utils with download function.
-* Added get_app_specific_directory to misc_utils.
+* Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
 * Added normalize_file_path to file_utils.
 
 
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 6bb4971ae..987595636 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -58,15 +58,21 @@ def search_for_file(file: str,
         return None if single else []
 
 
-def normalize_file_path(path: str, including_home_directory: bool = False) -> str:
+def normalize_file_path(path: str, home_directory: bool = True) -> str:
+    """
+    Normalizes the given file path name and returns. Does things like remove multiple
+    consecutive slashes and redundant/unnecessary parent paths; if the home_directory
+    argument is True (the default) then also handles the special tilde home directory
+    component/convention and uses this in the result if applicable.
+    """
     if not isinstance(path, str) or not path:
         path = os.getcwd()
     path = os.path.normpath(path)
-    home_directory = os.path.expanduser("~")
-    if path.startswith("~"):
+    home_directory = os.path.expanduser("~") if home_directory is True else None
+    if home_directory and path.startswith("~"):
         path = os.path.join(home_directory, path[2 if path.startswith("~/") else 1:])
     path = os.path.abspath(path)
-    if including_home_directory and (os.name == "posix"):
+    if home_directory and (os.name == "posix"):
         if path.startswith(home_directory) and path != home_directory:
             path = "~/" + pathlib.Path(path).relative_to(home_directory).as_posix()
     return path
diff --git a/dcicutils/http_utils.py b/dcicutils/http_utils.py
index a080dec06..305d2207d 100644
--- a/dcicutils/http_utils.py
+++ b/dcicutils/http_utils.py
@@ -6,6 +6,11 @@
 
 @contextmanager
 def download(url: str, suffix: Optional[str] = None, binary: bool = True) -> 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.
+    """
     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:
diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 6814dddd2..a66f34999 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -14,6 +14,7 @@
 import logging
 import math
 import os
+import platform
 import pytz
 import re
 import rfc3986.validators
@@ -2682,3 +2683,18 @@ def get_app_specific_directory() -> str:
     N.B. This is has been tested on MacOS and Linux but not on Windows.
     """
     return appdirs.user_data_dir()
+
+
+def get_os_name() -> str:
+    if os_name := platform.system():
+        if os_name == "Darwin": return "osx"  # noqa
+        elif os_name == "Linux": return "linux"  # noqa
+        elif os_name == "Windows": return "windows"  # noqa
+    return ""
+
+
+def get_cpu_architecture_name() -> str:
+    if os_architecture_name := platform.machine():
+        if os_architecture_name == "x86_64": return "amd64"  # noqa
+        return os_architecture_name
+    return ""
diff --git a/pyproject.toml b/pyproject.toml
index 9f64ef1d9..05fc10279 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b3"  # TODO: To become 8.8.5
+version = "8.8.4.1b4"  # 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"

From 5ddaee3e24e7ac9f1363147a5a044188c2f2d965 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 24 Apr 2024 10:37:58 -0400
Subject: [PATCH 07/46] Allow python 3.12

---
 CHANGELOG.rst          |    1 +
 dcicutils/zip_utils.py |    5 +
 poetry.lock            | 1892 ++++++++++++++++++++--------------------
 pyproject.toml         |   10 +-
 4 files changed, 974 insertions(+), 934 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 6fc32f569..7629094a7 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -17,6 +17,7 @@ Change Log
 * Added http_utils with download function.
 * Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
 * Added normalize_file_path to file_utils.
+* Allow Python 3.12 (pyproject.toml).
 
 
 8.8.4
diff --git a/dcicutils/zip_utils.py b/dcicutils/zip_utils.py
index a262ce549..93c5cfef7 100644
--- a/dcicutils/zip_utils.py
+++ b/dcicutils/zip_utils.py
@@ -51,6 +51,11 @@ def unpack_gz_file_to_temporary_file(file: str, suffix: Optional[str] = None) ->
 
 def extract_file_from_zip(zip_file: str, file_to_extract: str,
                           destination_file: str, raise_exception: bool = True) -> bool:
+    """
+    Extracts from the given zip file, the given file to extract, writing it to the
+    given destination file. Returns True if all is well, otherwise False, or if the
+    raise_exception argument is True (the default), then raises and exception on error.
+    """
     try:
         if not (destination_directory := os.path.dirname(destination_file)):
             destination_directory = os.getcwd()
diff --git a/poetry.lock b/poetry.lock
index 51d31667f..fb8013b34 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -13,32 +13,33 @@ files = [
 
 [[package]]
 name = "async-timeout"
-version = "4.0.2"
+version = "4.0.3"
 description = "Timeout context manager for asyncio programs"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "async-timeout-4.0.2.tar.gz", hash = "sha256:2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15"},
-    {file = "async_timeout-4.0.2-py3-none-any.whl", hash = "sha256:8ca1e4fcf50d07413d66d1a5e416e42cfdf5851c981d679a09851a6853383b3c"},
+    {file = "async-timeout-4.0.3.tar.gz", hash = "sha256:4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f"},
+    {file = "async_timeout-4.0.3-py3-none-any.whl", hash = "sha256:7405140ff1230c310e51dc27b3145b9092d659ce68ff733fb0cefe3ee42be028"},
 ]
 
 [[package]]
 name = "attrs"
-version = "23.1.0"
+version = "23.2.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.1.0-py3-none-any.whl", hash = "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04"},
-    {file = "attrs-23.1.0.tar.gz", hash = "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015"},
+    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
+    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
 ]
 
 [package.extras]
 cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[docs,tests]", "pre-commit"]
+dev = ["attrs[tests]", "pre-commit"]
 docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
 tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
+tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
 
 [[package]]
 name = "aws-requests-auth"
@@ -56,50 +57,53 @@ requests = ">=0.14.0"
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.12.2"
+version = "4.12.3"
 description = "Screen-scraping library"
 optional = false
 python-versions = ">=3.6.0"
 files = [
-    {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
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 description = "Low-level, data-driven core of boto 3."
 optional = false
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 [package.extras]
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 [package.dependencies]
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 typing-extensions = {version = ">=4.1.0", markers = "python_version < \"3.9\""}
 
+[package.extras]
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+
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 [package.dependencies]
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 [package.dependencies]
@@ -776,34 +804,34 @@ toml = ["tomli"]
 
 [[package]]
 name = "cryptography"
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 description = "cryptography is a package which provides cryptographic recipes and primitives to Python developers."
 optional = false
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+    {file = "cryptography-41.0.7.tar.gz", hash = "sha256:13f93ce9bea8016c253b34afc6bd6a75993e5c40672ed5405a9c832f0d4a00bc"},
 ]
 
 [package.dependencies]
@@ -874,13 +902,13 @@ files = [
 
 [[package]]
 name = "exceptiongroup"
-version = "1.1.2"
+version = "1.2.1"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.1.2-py3-none-any.whl", hash = "sha256:e346e69d186172ca7cf029c8c1d16235aa0e04035e5750b4b95039e65204328f"},
-    {file = "exceptiongroup-1.1.2.tar.gz", hash = "sha256:12c3e887d6485d16943a309616de20ae5582633e0a2eda17f4e10fd61c1e8af5"},
+    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
+    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
 ]
 
 [package.extras]
@@ -904,24 +932,24 @@ pyflakes = ">=2.5.0,<2.6.0"
 
 [[package]]
 name = "flaky"
-version = "3.7.0"
-description = "Plugin for nose or pytest that automatically reruns flaky tests."
+version = "3.8.1"
+description = "Plugin for pytest that automatically reruns flaky tests."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.5"
 files = [
-    {file = "flaky-3.7.0-py2.py3-none-any.whl", hash = "sha256:d6eda73cab5ae7364504b7c44670f70abed9e75f77dd116352f662817592ec9c"},
-    {file = "flaky-3.7.0.tar.gz", hash = "sha256:3ad100780721a1911f57a165809b7ea265a7863305acb66708220820caf8aa0d"},
+    {file = "flaky-3.8.1-py2.py3-none-any.whl", hash = "sha256:194ccf4f0d3a22b2de7130f4b62e45e977ac1b5ccad74d4d48f3005dcc38815e"},
+    {file = "flaky-3.8.1.tar.gz", hash = "sha256:47204a81ec905f3d5acfbd61daeabcada8f9d4031616d9bcb0618461729699f5"},
 ]
 
 [[package]]
 name = "gitdb"
-version = "4.0.10"
+version = "4.0.11"
 description = "Git Object Database"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "gitdb-4.0.10-py3-none-any.whl", hash = "sha256:c286cf298426064079ed96a9e4a9d39e7f3e9bf15ba60701e95f5492f28415c7"},
-    {file = "gitdb-4.0.10.tar.gz", hash = "sha256:6eb990b69df4e15bad899ea868dc46572c3f75339735663b81de79b06f17eb9a"},
+    {file = "gitdb-4.0.11-py3-none-any.whl", hash = "sha256:81a3407ddd2ee8df444cbacea00e2d038e40150acfa3001696fe0dcf1d3adfa4"},
+    {file = "gitdb-4.0.11.tar.gz", hash = "sha256:bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b"},
 ]
 
 [package.dependencies]
@@ -929,27 +957,31 @@ smmap = ">=3.0.1,<6"
 
 [[package]]
 name = "gitpython"
-version = "3.1.32"
+version = "3.1.43"
 description = "GitPython is a Python library used to interact with Git repositories"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "GitPython-3.1.32-py3-none-any.whl", hash = "sha256:e3d59b1c2c6ebb9dfa7a184daf3b6dd4914237e7488a1730a6d8f6f5d0b4187f"},
-    {file = "GitPython-3.1.32.tar.gz", hash = "sha256:8d9b8cb1e80b9735e8717c9362079d3ce4c6e5ddeebedd0361b228c3a67a62f6"},
+    {file = "GitPython-3.1.43-py3-none-any.whl", hash = "sha256:eec7ec56b92aad751f9912a73404bc02ba212a23adb2c7098ee668417051a1ff"},
+    {file = "GitPython-3.1.43.tar.gz", hash = "sha256:35f314a9f878467f5453cc1fee295c3e18e52f1b99f10f6cf5b1682e968a9e7c"},
 ]
 
 [package.dependencies]
 gitdb = ">=4.0.1,<5"
 
+[package.extras]
+doc = ["sphinx (==4.3.2)", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "sphinxcontrib-applehelp (>=1.0.2,<=1.0.4)", "sphinxcontrib-devhelp (==1.0.2)", "sphinxcontrib-htmlhelp (>=2.0.0,<=2.0.1)", "sphinxcontrib-qthelp (==1.0.3)", "sphinxcontrib-serializinghtml (==1.1.5)"]
+test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions"]
+
 [[package]]
 name = "hupper"
-version = "1.12"
+version = "1.12.1"
 description = "Integrated process monitor for developing and reloading daemons."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "hupper-1.12-py3-none-any.whl", hash = "sha256:b8bc41bb75939e816f30f118026d0ba99544af4d6992583df3b4813765af27ef"},
-    {file = "hupper-1.12.tar.gz", hash = "sha256:18b1653d9832c9f8e7d3401986c7e7af2ae6783616be0bc406bfe0b14134a5c6"},
+    {file = "hupper-1.12.1-py3-none-any.whl", hash = "sha256:e872b959f09d90be5fb615bd2e62de89a0b57efc037bdf9637fb09cdf8552b19"},
+    {file = "hupper-1.12.1.tar.gz", hash = "sha256:06bf54170ff4ecf4c84ad5f188dee3901173ab449c2608ad05b9bfd6b13e32eb"},
 ]
 
 [package.extras]
@@ -958,24 +990,24 @@ testing = ["mock", "pytest", "pytest-cov", "watchdog"]
 
 [[package]]
 name = "idna"
-version = "3.4"
+version = "3.7"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
 python-versions = ">=3.5"
 files = [
-    {file = "idna-3.4-py3-none-any.whl", hash = "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2"},
-    {file = "idna-3.4.tar.gz", hash = "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4"},
+    {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"},
+    {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"},
 ]
 
 [[package]]
 name = "importlib-resources"
-version = "6.1.0"
+version = "6.4.0"
 description = "Read resources from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "importlib_resources-6.1.0-py3-none-any.whl", hash = "sha256:aa50258bbfa56d4e33fbd8aa3ef48ded10d1735f11532b8df95388cc6bdb7e83"},
-    {file = "importlib_resources-6.1.0.tar.gz", hash = "sha256:9d48dcccc213325e810fd723e7fbb45ccb39f6cf5c31f00cf2b965f5f10f3cb9"},
+    {file = "importlib_resources-6.4.0-py3-none-any.whl", hash = "sha256:50d10f043df931902d4194ea07ec57960f66a80449ff867bfe782b4c486ba78c"},
+    {file = "importlib_resources-6.4.0.tar.gz", hash = "sha256:cdb2b453b8046ca4e3798eb1d84f3cce1446a0e8e7b5ef4efb600f19fc398145"},
 ]
 
 [package.dependencies]
@@ -983,7 +1015,7 @@ zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
+testing = ["jaraco.test (>=5.4)", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-ruff (>=0.2.1)", "zipp (>=3.17)"]
 
 [[package]]
 name = "iniconfig"
@@ -1020,13 +1052,13 @@ files = [
 
 [[package]]
 name = "jsonschema"
-version = "4.19.1"
+version = "4.21.1"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema-4.19.1-py3-none-any.whl", hash = "sha256:cd5f1f9ed9444e554b38ba003af06c0a8c2868131e56bfbef0550fb450c0330e"},
-    {file = "jsonschema-4.19.1.tar.gz", hash = "sha256:ec84cc37cfa703ef7cd4928db24f9cb31428a5d0fa77747b8b51a847458e0bbf"},
+    {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
+    {file = "jsonschema-4.21.1.tar.gz", hash = "sha256:85727c00279f5fa6bedbe6238d2aa6403bedd8b4864ab11207d07df3cc1b2ee5"},
 ]
 
 [package.dependencies]
@@ -1043,18 +1075,18 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2023.7.1"
+version = "2023.12.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "jsonschema_specifications-2023.7.1-py3-none-any.whl", hash = "sha256:05adf340b659828a004220a9613be00fa3f223f2b82002e273dee62fd50524b1"},
-    {file = "jsonschema_specifications-2023.7.1.tar.gz", hash = "sha256:c91a50404e88a1f6ba40636778e2ee08f6e24c5613fe4c53ac24578a5a7f72bb"},
+    {file = "jsonschema_specifications-2023.12.1-py3-none-any.whl", hash = "sha256:87e4fdf3a94858b8a2ba2778d9ba57d8a9cafca7c7489c46ba0d30a8bc6a9c3c"},
+    {file = "jsonschema_specifications-2023.12.1.tar.gz", hash = "sha256:48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc"},
 ]
 
 [package.dependencies]
 importlib-resources = {version = ">=1.4.0", markers = "python_version < \"3.9\""}
-referencing = ">=0.28.0"
+referencing = ">=0.31.0"
 
 [[package]]
 name = "mccabe"
@@ -1069,13 +1101,13 @@ files = [
 
 [[package]]
 name = "mirakuru"
-version = "2.5.1"
+version = "2.5.2"
 description = "Process executor (not only) for tests."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "mirakuru-2.5.1-py3-none-any.whl", hash = "sha256:0a16f897841741f8cd784f790e54d74e61456ba36be9cb9de731b49e2e7a45dc"},
-    {file = "mirakuru-2.5.1.tar.gz", hash = "sha256:5a60d641fa92c8bfcd383f6e52f7a0bf3f081da0467fc6e3e6a3f6b3e3e47a7b"},
+    {file = "mirakuru-2.5.2-py3-none-any.whl", hash = "sha256:90c2d90a8cf14349b2f33e6db30a16acd855499811e0312e56cf80ceacf2d3e5"},
+    {file = "mirakuru-2.5.2.tar.gz", hash = "sha256:41ca583d355eb7a6cfdc21c1aea549979d685c27b57239b88725434f115a7132"},
 ]
 
 [package.dependencies]
@@ -1097,13 +1129,13 @@ et-xmlfile = "*"
 
 [[package]]
 name = "opensearch-py"
-version = "2.3.0"
+version = "2.5.0"
 description = "Python client for OpenSearch"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,<4,>=2.7"
 files = [
-    {file = "opensearch-py-2.3.0.tar.gz", hash = "sha256:493b224d0f865f62663f689c3a7662b1edccf9ee6c7643f2561cafda04e3a66a"},
-    {file = "opensearch_py-2.3.0-py2.py3-none-any.whl", hash = "sha256:4093d0bbe575979d67cfd74a153eb91d82e354e232d76c6980876321c73056c1"},
+    {file = "opensearch-py-2.5.0.tar.gz", hash = "sha256:0dde4ac7158a717d92a8cd81964cb99705a4b80bcf9258ba195b9a9f23f5226d"},
+    {file = "opensearch_py-2.5.0-py2.py3-none-any.whl", hash = "sha256:cf093a40e272b60663f20417fc1264ac724dcf1e03c1a4542a6b44835b1e6c49"},
 ]
 
 [package.dependencies]
@@ -1111,23 +1143,23 @@ certifi = ">=2022.12.07"
 python-dateutil = "*"
 requests = ">=2.4.0,<3.0.0"
 six = "*"
-urllib3 = ">=1.21.1,<2"
+urllib3 = ">=1.26.18,<2"
 
 [package.extras]
 async = ["aiohttp (>=3,<4)"]
-develop = ["black", "botocore", "coverage (<7.0.0)", "jinja2", "mock", "myst-parser", "pytest (>=3.0.0)", "pytest-cov", "pytest-mock (<4.0.0)", "pytz", "pyyaml", "requests (>=2.0.0,<3.0.0)", "sphinx", "sphinx-copybutton", "sphinx-rtd-theme"]
-docs = ["myst-parser", "sphinx", "sphinx-copybutton", "sphinx-rtd-theme"]
+develop = ["black", "botocore", "coverage (<8.0.0)", "jinja2", "mock", "myst-parser", "pytest (>=3.0.0)", "pytest-cov", "pytest-mock (<4.0.0)", "pytz", "pyyaml", "requests (>=2.0.0,<3.0.0)", "sphinx", "sphinx-copybutton", "sphinx-rtd-theme"]
+docs = ["aiohttp (>=3,<4)", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-rtd-theme"]
 kerberos = ["requests-kerberos"]
 
 [[package]]
 name = "packaging"
-version = "23.1"
+version = "24.0"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "packaging-23.1-py3-none-any.whl", hash = "sha256:994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61"},
-    {file = "packaging-23.1.tar.gz", hash = "sha256:a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f"},
+    {file = "packaging-24.0-py3-none-any.whl", hash = "sha256:2ddfb553fdf02fb784c234c7ba6ccc288296ceabec964ad2eae3777778130bc5"},
+    {file = "packaging-24.0.tar.gz", hash = "sha256:eb82c5e3e56209074766e6885bb04b8c38a0c015d0a30036ebe7ece34c9989e9"},
 ]
 
 [[package]]
@@ -1148,13 +1180,13 @@ testing = ["Paste", "pytest", "pytest-cov"]
 
 [[package]]
 name = "pip-licenses"
-version = "4.3.3"
+version = "4.4.0"
 description = "Dump the software license list of Python packages installed with pip."
 optional = false
 python-versions = "~=3.8"
 files = [
-    {file = "pip-licenses-4.3.3.tar.gz", hash = "sha256:d14447094135eb5e43e4d9e1e3bcdb17a05751a9199df2d07f043a542c241c7a"},
-    {file = "pip_licenses-4.3.3-py3-none-any.whl", hash = "sha256:1b697cace3149d7d380307bb1f1e0505f0db98f25fada64d32b7e6240f37f72c"},
+    {file = "pip-licenses-4.4.0.tar.gz", hash = "sha256:996817118375445243a34faafe23c06f6b2d250247c4046571b5a6722d45be69"},
+    {file = "pip_licenses-4.4.0-py3-none-any.whl", hash = "sha256:dbad2ac5a25f574cabe2716f2f031a0c5fa359bed9b3ef615301f4e546893b46"},
 ]
 
 [package.dependencies]
@@ -1209,13 +1241,13 @@ testing = ["pytest", "pytest-cov"]
 
 [[package]]
 name = "pluggy"
-version = "1.2.0"
+version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
@@ -1224,53 +1256,55 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "port-for"
-version = "0.7.1"
+version = "0.7.2"
 description = "Utility that helps with local TCP ports management. It can find an unused TCP localhost port and remember the association."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "prettytable"
-version = "3.9.0"
+version = "3.10.0"
 description = "A simple Python library for easily displaying tabular data in a visually appealing ASCII table format"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 wcwidth = "*"
 
 [package.extras]
-tests = ["pytest", "pytest-cov", "pytest-lazy-fixture"]
+tests = ["pytest", "pytest-cov", "pytest-lazy-fixtures"]
 
 [[package]]
 name = "psutil"
-version = "5.9.5"
+version = "5.9.8"
 description = "Cross-platform lib for process and system monitoring in Python."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
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+    {file = "psutil-5.9.8-cp37-abi3-win32.whl", hash = "sha256:bc56c2a1b0d15aa3eaa5a60c9f3f8e3e565303b465dbf57a1b730e7a2b9844e0"},
+    {file = "psutil-5.9.8-cp37-abi3-win_amd64.whl", hash = "sha256:8db4c1b57507eef143a15a6884ca10f7c73876cdf5d51e713151c1236a0e68cf"},
+    {file = "psutil-5.9.8-cp38-abi3-macosx_11_0_arm64.whl", hash = "sha256:d16bbddf0693323b8c6123dd804100241da461e41d6e332fb0ba6058f630f8c8"},
+    {file = "psutil-5.9.8.tar.gz", hash = "sha256:6be126e3225486dff286a8fb9a06246a5253f4c7c53b475ea5f5ac934e64194c"},
 ]
 
 [package.extras]
@@ -1289,13 +1323,13 @@ files = [
 
 [[package]]
 name = "pycparser"
-version = "2.21"
+version = "2.22"
 description = "C parser in Python"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
+python-versions = ">=3.8"
 files = [
-    {file = "pycparser-2.21-py2.py3-none-any.whl", hash = "sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9"},
-    {file = "pycparser-2.21.tar.gz", hash = "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"},
+    {file = "pycparser-2.22-py3-none-any.whl", hash = "sha256:c3702b6d3dd8c7abc1afa565d7e63d53a1d0bd86cdc24edd75470f4de499cfcc"},
+    {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"},
 ]
 
 [[package]]
@@ -1328,20 +1362,20 @@ tests = ["coverage[toml] (==5.0.4)", "pytest (>=6.0.0,<7.0.0)"]
 
 [[package]]
 name = "pyopenssl"
-version = "23.2.0"
+version = "23.3.0"
 description = "Python wrapper module around the OpenSSL library"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
-    {file = "pyOpenSSL-23.2.0-py3-none-any.whl", hash = "sha256:24f0dc5227396b3e831f4c7f602b950a5e9833d292c8e4a2e06b709292806ae2"},
-    {file = "pyOpenSSL-23.2.0.tar.gz", hash = "sha256:276f931f55a452e7dea69c7173e984eb2a4407ce413c918aa34b55f82f9b8bac"},
+    {file = "pyOpenSSL-23.3.0-py3-none-any.whl", hash = "sha256:6756834481d9ed5470f4a9393455154bc92fe7a64b7bc6ee2c804e78c52099b2"},
+    {file = "pyOpenSSL-23.3.0.tar.gz", hash = "sha256:6b2cba5cc46e822750ec3e5a81ee12819850b11303630d575e98108a079c2b12"},
 ]
 
 [package.dependencies]
-cryptography = ">=38.0.0,<40.0.0 || >40.0.0,<40.0.1 || >40.0.1,<42"
+cryptography = ">=41.0.5,<42"
 
 [package.extras]
-docs = ["sphinx (!=5.2.0,!=5.2.0.post0)", "sphinx-rtd-theme"]
+docs = ["sphinx (!=5.2.0,!=5.2.0.post0,!=7.2.5)", "sphinx-rtd-theme"]
 test = ["flaky", "pretend", "pytest (>=3.0.1)"]
 
 [[package]]
@@ -1382,13 +1416,13 @@ testing = ["coverage", "nose", "virtualenv", "webtest (>=1.3.1)", "zope.componen
 
 [[package]]
 name = "pytest"
-version = "7.4.2"
+version = "7.4.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-7.4.2-py3-none-any.whl", hash = "sha256:1d881c6124e08ff0a1bb75ba3ec0bfd8b5354a01c194ddd5a0a870a48d99b002"},
-    {file = "pytest-7.4.2.tar.gz", hash = "sha256:a766259cfab564a2ad52cb1aae1b881a75c3eb7e34ca3779697c23ed47c47069"},
+    {file = "pytest-7.4.4-py3-none-any.whl", hash = "sha256:b090cdf5ed60bf4c45261be03239c2c1c22df034fbffe691abe93cd80cea01d8"},
+    {file = "pytest-7.4.4.tar.gz", hash = "sha256:2cf0005922c6ace4a3e2ec8b4080eb0d9753fdc93107415332f50ce9e7994280"},
 ]
 
 [package.dependencies]
@@ -1404,13 +1438,13 @@ testing = ["argcomplete", "attrs (>=19.2.0)", "hypothesis (>=3.56)", "mock", "no
 
 [[package]]
 name = "pytest-cov"
-version = "4.1.0"
+version = "5.0.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pytest-cov-4.1.0.tar.gz", hash = "sha256:3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6"},
-    {file = "pytest_cov-4.1.0-py3-none-any.whl", hash = "sha256:6ba70b9e97e69fcc3fb45bfeab2d0a138fb65c4d0d6a41ef33983ad114be8c3a"},
+    {file = "pytest-cov-5.0.0.tar.gz", hash = "sha256:5837b58e9f6ebd335b0f8060eecce69b662415b16dc503883a02f45dfeb14857"},
+    {file = "pytest_cov-5.0.0-py3-none-any.whl", hash = "sha256:4f0764a1219df53214206bf1feea4633c3b558a2925c8b59f144f682861ce652"},
 ]
 
 [package.dependencies]
@@ -1418,21 +1452,21 @@ coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
+testing = ["fields", "hunter", "process-tests", "pytest-xdist", "virtualenv"]
 
 [[package]]
 name = "pytest-mock"
-version = "3.11.1"
+version = "3.14.0"
 description = "Thin-wrapper around the mock package for easier use with pytest"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "pytest-mock-3.11.1.tar.gz", hash = "sha256:7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f"},
-    {file = "pytest_mock-3.11.1-py3-none-any.whl", hash = "sha256:21c279fff83d70763b05f8874cc9cfb3fcacd6d354247a976f9529d19f9acf39"},
+    {file = "pytest-mock-3.14.0.tar.gz", hash = "sha256:2719255a1efeceadbc056d6bf3df3d1c5015530fb40cf347c0f9afac88410bd0"},
+    {file = "pytest_mock-3.14.0-py3-none-any.whl", hash = "sha256:0b72c38033392a5f4621342fe11e9219ac11ec9d375f8e2a0c164539e0d70f6f"},
 ]
 
 [package.dependencies]
-pytest = ">=5.0"
+pytest = ">=6.2.5"
 
 [package.extras]
 dev = ["pre-commit", "pytest-asyncio", "tox"]
@@ -1456,13 +1490,13 @@ redis = ">=3"
 
 [[package]]
 name = "pytest-runner"
-version = "6.0.0"
+version = "6.0.1"
 description = "Invoke py.test as distutils command with dependency resolution"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "pytest-runner-6.0.0.tar.gz", hash = "sha256:b4d85362ed29b4c348678de797df438f0f0509497ddb8c647096c02a6d87b685"},
-    {file = "pytest_runner-6.0.0-py3-none-any.whl", hash = "sha256:4c059cf11cf4306e369c0f8f703d1eaf8f32fad370f41deb5f007044656aca6b"},
+    {file = "pytest-runner-6.0.1.tar.gz", hash = "sha256:70d4739585a7008f37bf4933c013fdb327b8878a5a69fcbb3316c88882f0f49b"},
+    {file = "pytest_runner-6.0.1-py3-none-any.whl", hash = "sha256:ea326ed6f6613992746062362efab70212089a4209c08d67177b3df1c52cd9f2"},
 ]
 
 [package.extras]
@@ -1471,13 +1505,13 @@ testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)",
 
 [[package]]
 name = "python-dateutil"
-version = "2.8.2"
+version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
-    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
+    {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
+    {file = "python_dateutil-2.9.0.post0-py2.py3-none-any.whl", hash = "sha256:a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427"},
 ]
 
 [package.dependencies]
@@ -1485,13 +1519,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2023.3"
+version = "2024.1"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2023.3-py2.py3-none-any.whl", hash = "sha256:a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb"},
-    {file = "pytz-2023.3.tar.gz", hash = "sha256:1d8ce29db189191fb55338ee6d0387d82ab59f3d00eac103412d64e0ebd0c588"},
+    {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
+    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
 ]
 
 [[package]]
@@ -1584,13 +1618,13 @@ ocsp = ["cryptography (>=36.0.1)", "pyopenssl (==20.0.1)", "requests (>=2.26.0)"
 
 [[package]]
 name = "referencing"
-version = "0.30.2"
+version = "0.35.0"
 description = "JSON Referencing + Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "referencing-0.30.2-py3-none-any.whl", hash = "sha256:449b6669b6121a9e96a7f9e410b245d471e8d48964c67113ce9afe50c8dd7bdf"},
-    {file = "referencing-0.30.2.tar.gz", hash = "sha256:794ad8003c65938edcdbc027f1933215e0d0ccc0291e3ce20a4d87432b59efc0"},
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+    {file = "referencing-0.35.0.tar.gz", hash = "sha256:191e936b0c696d0af17ad7430a3dc68e88bc11be6514f4757dc890f04ab05889"},
 ]
 
 [package.dependencies]
@@ -1634,144 +1668,144 @@ idna2008 = ["idna"]
 
 [[package]]
 name = "rpds-py"
-version = "0.10.6"
+version = "0.18.0"
 description = "Python bindings to Rust's persistent data structures (rpds)"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "s3transfer"
-version = "0.7.0"
+version = "0.10.1"
 description = "An Amazon S3 Transfer Manager"
 optional = false
-python-versions = ">= 3.7"
+python-versions = ">= 3.8"
 files = [
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 ]
 
 [package.dependencies]
-botocore = ">=1.12.36,<2.0a.0"
+botocore = ">=1.33.2,<2.0a.0"
 
 [package.extras]
-crt = ["botocore[crt] (>=1.20.29,<2.0a.0)"]
+crt = ["botocore[crt] (>=1.33.2,<2.0a.0)"]
 
 [[package]]
 name = "setuptools"
-version = "69.0.2"
+version = "69.5.1"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
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-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "flake8-2020", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "pip (>=19.1)", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf", "pytest-ruff", "pytest-timeout", "pytest-xdist", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.1)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
+testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -1786,24 +1820,24 @@ files = [
 
 [[package]]
 name = "smmap"
-version = "5.0.0"
+version = "5.0.1"
 description = "A pure Python implementation of a sliding window memory map manager"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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+    {file = "smmap-5.0.1.tar.gz", hash = "sha256:dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62"},
 ]
 
 [[package]]
 name = "soupsieve"
-version = "2.4.1"
+version = "2.5"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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+    {file = "soupsieve-2.5.tar.gz", hash = "sha256:5663d5a7b3bfaeee0bc4372e7fc48f9cff4940b3eec54a6451cc5299f1097690"},
 ]
 
 [[package]]
@@ -1884,50 +1918,50 @@ docs = ["Sphinx (>=1.3.1)", "docutils", "pylons-sphinx-themes"]
 
 [[package]]
 name = "types-awscrt"
-version = "0.19.3"
+version = "0.20.9"
 description = "Type annotations and code completion for awscrt"
 optional = false
-python-versions = ">=3.7,<4.0"
+python-versions = "<4.0,>=3.7"
 files = [
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+    {file = "types_awscrt-0.20.9-py3-none-any.whl", hash = "sha256:3ae374b553e7228ba41a528cf42bd0b2ad7303d806c73eff4aaaac1515e3ea4e"},
+    {file = "types_awscrt-0.20.9.tar.gz", hash = "sha256:64898a2f4a2468f66233cb8c29c5f66de907cf80ba1ef5bb1359aef2f81bb521"},
 ]
 
 [[package]]
 name = "types-s3transfer"
-version = "0.7.0"
+version = "0.10.1"
 description = "Type annotations and code completion for s3transfer"
 optional = false
-python-versions = ">=3.7,<4.0"
+python-versions = "<4.0,>=3.8"
 files = [
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+    {file = "types_s3transfer-0.10.1-py3-none-any.whl", hash = "sha256:49a7c81fa609ac1532f8de3756e64b58afcecad8767933310228002ec7adff74"},
+    {file = "types_s3transfer-0.10.1.tar.gz", hash = "sha256:02154cce46528287ad76ad1a0153840e0492239a0887e8833466eccf84b98da0"},
 ]
 
 [[package]]
 name = "typing-extensions"
-version = "4.7.1"
-description = "Backported and Experimental Type Hints for Python 3.7+"
+version = "4.11.0"
+description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "urllib3"
-version = "1.26.16"
+version = "1.26.18"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 files = [
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+    {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"},
+    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
 ]
 
 [package.extras]
-brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
+brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"]
 secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
@@ -1948,28 +1982,28 @@ testing = ["coverage", "pytest", "pytest-cov"]
 
 [[package]]
 name = "waitress"
-version = "2.1.2"
+version = "3.0.0"
 description = "Waitress WSGI server"
 optional = false
-python-versions = ">=3.7.0"
+python-versions = ">=3.8.0"
 files = [
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+    {file = "waitress-3.0.0-py3-none-any.whl", hash = "sha256:2a06f242f4ba0cc563444ca3d1998959447477363a2d7e9b8b4d75d35cfd1669"},
+    {file = "waitress-3.0.0.tar.gz", hash = "sha256:005da479b04134cdd9dd602d1ee7c49d79de0537610d653674cc6cbde222b8a1"},
 ]
 
 [package.extras]
 docs = ["Sphinx (>=1.8.1)", "docutils", "pylons-sphinx-themes (>=1.0.9)"]
-testing = ["coverage (>=5.0)", "pytest", "pytest-cover"]
+testing = ["coverage (>=5.0)", "pytest", "pytest-cov"]
 
 [[package]]
 name = "wcwidth"
-version = "0.2.8"
+version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
 files = [
-    {file = "wcwidth-0.2.8-py2.py3-none-any.whl", hash = "sha256:77f719e01648ed600dfa5402c347481c0992263b81a027344f3e1ba25493a704"},
-    {file = "wcwidth-0.2.8.tar.gz", hash = "sha256:8705c569999ffbb4f6a87c6d1b80f324bd6db952f5eb0b95bc07517f4c1813d4"},
+    {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
+    {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
 ]
 
 [[package]]
@@ -1989,17 +2023,17 @@ testing = ["coverage", "pytest (>=3.1.0)", "pytest-cov", "pytest-xdist"]
 
 [[package]]
 name = "websocket-client"
-version = "1.6.1"
+version = "1.8.0"
 description = "WebSocket client for Python with low level API options"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "websocket-client-1.6.1.tar.gz", hash = "sha256:c951af98631d24f8df89ab1019fc365f2227c0892f12fd150e935607c79dd0dd"},
-    {file = "websocket_client-1.6.1-py3-none-any.whl", hash = "sha256:f1f9f2ad5291f0225a49efad77abf9e700b6fef553900623060dad6e26503b9d"},
+    {file = "websocket_client-1.8.0-py3-none-any.whl", hash = "sha256:17b44cc997f5c498e809b22cdf2d9c7a9e71c02c8cc2b6c56e7c2d1239bfa526"},
+    {file = "websocket_client-1.8.0.tar.gz", hash = "sha256:3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da"},
 ]
 
 [package.extras]
-docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"]
+docs = ["Sphinx (>=6.0)", "myst-parser (>=2.0.0)", "sphinx-rtd-theme (>=1.1.0)"]
 optional = ["python-socks", "wsaccel"]
 test = ["websockets"]
 
@@ -2026,18 +2060,18 @@ tests = ["PasteDeploy", "WSGIProxy2", "coverage", "mock", "nose (<1.3.0)", "pyqu
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.18.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]
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 [[package]]
 name = "zope-deprecation"
@@ -2059,47 +2093,47 @@ test = ["zope.testrunner"]
 
 [[package]]
 name = "zope-interface"
-version = "6.1"
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 description = "Interfaces for Python"
 optional = false
 python-versions = ">=3.7"
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+    {file = "zope.interface-6.3.tar.gz", hash = "sha256:f83d6b4b22262d9a826c3bd4b2fbfafe1d0000f085ef8e44cd1328eea274ae6a"},
 ]
 
 [package.dependencies]
@@ -2112,5 +2146,5 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = ">=3.8,<3.12"
-content-hash = "87d855b9552dbd71f3afc072689b548b0eb7b540a4decee3a6f6993312a84fac"
+python-versions = ">=3.8,<3.13"
+content-hash = "3ff0434deeb048d183ca5e6d0ce5d931be4718f18cb6ccebf6250e2edf0aafdb"
diff --git a/pyproject.toml b/pyproject.toml
index 05fc10279..6b1fc1114 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,9 +37,9 @@ classifiers = [
 
 
 [tool.poetry.dependencies]
-python = ">=3.8,<3.12"
-boto3 = "^1.28.57"
-botocore = "^1.31.57"
+python = ">=3.8,<3.13"
+boto3 = "^1.34.90"
+botocore = "^1.34.90"
 # 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"
@@ -70,8 +70,8 @@ webtest = "^2.0.34"
 
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.28.57"
-botocore-stubs = "^1.31.57"
+boto3-stubs = "^1.34.90"
+botocore-stubs = "^1.34.90"
 coverage = ">=7.2.3"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023

From df9d5e2db39dd25ab71202e09189619db4411ce3 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 24 Apr 2024 12:43:30 -0400
Subject: [PATCH 08/46] minor fix to misc_utils.create_dict

---
 CHANGELOG.rst           | 10 ++++++----
 dcicutils/misc_utils.py |  2 +-
 pyproject.toml          |  2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 7629094a7..d9ea6d3a9 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,11 +13,13 @@ Change Log
 * Added check for ES_HOST_LOCAL environment variable in ff_utils.get_es_metadata;
   for running Foursight checks locally (with local ssh tunnel to ES proxy);
   came up in foursight/checks/audit_checks (2024-04-23).
-* Added extract_file_from_zip to zip_utils.
-* Added http_utils with download function.
-* Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
-* Added normalize_file_path to file_utils.
 * Allow Python 3.12 (pyproject.toml).
+* Few general things initially related to rclone support in smaht-submitr:
+  - Added extract_file_from_zip to zip_utils.
+  - Added http_utils with download function.
+  - Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
+  - Added normalize_file_path to file_utils.
+  - Minor fix to misc_utils.create_dict.
 
 
 8.8.4
diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index a66f34999..34b8fc320 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -1524,7 +1524,7 @@ def right_trim(list_or_tuple: Union[List[Any], Tuple[Any]],
 def create_dict(**kwargs) -> dict:
     result = {}
     for name in kwargs:
-        if kwargs[name]:
+        if not (kwargs[name] is None):
             result[name] = kwargs[name]
     return result
 
diff --git a/pyproject.toml b/pyproject.toml
index 6b1fc1114..149e90d11 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b4"  # TODO: To become 8.8.5
+version = "8.8.4.1b5"  # 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"

From d9a5b9e0f763cf40486e17697cd0fc1786fc4d4a Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 24 Apr 2024 19:01:24 -0400
Subject: [PATCH 09/46] couple new functions in tmpfile_utils

---
 CHANGELOG.rst              |  3 ++-
 dcicutils/tmpfile_utils.py | 26 ++++++++++++++++++++++++++
 2 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index d9ea6d3a9..0306c7cf5 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -19,7 +19,8 @@ Change Log
   - Added http_utils with download function.
   - Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
   - Added normalize_file_path to file_utils.
-  - Minor fix to misc_utils.create_dict.
+  - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
+  - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
 
 
 8.8.4
diff --git a/dcicutils/tmpfile_utils.py b/dcicutils/tmpfile_utils.py
index f96ec4ef1..9e6301961 100644
--- a/dcicutils/tmpfile_utils.py
+++ b/dcicutils/tmpfile_utils.py
@@ -26,6 +26,9 @@ def temporary_file(name: Optional[str] = None, suffix: Optional[str] = None,
 
 
 def remove_temporary_directory(tmp_directory_name: str) -> None:
+    """
+    Removes the given directory, recursively; but ONLY if it is (somewhere) within the system temporary directory.
+    """
     def is_temporary_directory(path: str) -> bool:
         try:
             tmpdir = tempfile.gettempdir()
@@ -34,3 +37,26 @@ def is_temporary_directory(path: str) -> bool:
             return False
     if is_temporary_directory(tmp_directory_name):  # Guard against errant deletion.
         shutil.rmtree(tmp_directory_name)
+
+
+def create_temporary_file_name(suffix: Optional[str] = None) -> str:
+    """
+    Generates and returns the full path to file within the system temporary directory.
+    """
+    with tempfile.NamedTemporaryFile(suffix=suffix, delete=False) as tmp_file:
+        tmp_file_name = tmp_file.name
+    return tmp_file_name
+
+
+def remove_temporary_file(tmp_file_name: str) -> bool:
+    """
+    Removes the given file; but ONLY if it is (somewhere) within the system temporary directory.
+    """
+    try:
+        tmpdir = tempfile.gettempdir()
+        if (os.path.commonpath([tmpdir, tmp_file_name]) == tmpdir) and os.path.isfile(tmp_file_name):
+            os.remove(tmp_file_name)
+            return True
+        return False
+    except Exception:
+        return False

From 407b4d08a15a5b4898d79acf98d028f7ebe568c6 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 24 Apr 2024 19:01:32 -0400
Subject: [PATCH 10/46] version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 149e90d11..972b91b36 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b5"  # TODO: To become 8.8.5
+version = "8.8.4.1b6"  # 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"

From 4d9a4a8bd37369fce932f1f898643102f92f4cdd Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 24 Apr 2024 19:15:21 -0400
Subject: [PATCH 11/46] version

---
 dcicutils/tmpfile_utils.py | 4 ++--
 pyproject.toml             | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/dcicutils/tmpfile_utils.py b/dcicutils/tmpfile_utils.py
index 9e6301961..68303da92 100644
--- a/dcicutils/tmpfile_utils.py
+++ b/dcicutils/tmpfile_utils.py
@@ -39,11 +39,11 @@ def is_temporary_directory(path: str) -> bool:
         shutil.rmtree(tmp_directory_name)
 
 
-def create_temporary_file_name(suffix: Optional[str] = None) -> str:
+def create_temporary_file_name(prefix: Optional[str] = None, suffix: Optional[str] = None) -> str:
     """
     Generates and returns the full path to file within the system temporary directory.
     """
-    with tempfile.NamedTemporaryFile(suffix=suffix, delete=False) as tmp_file:
+    with tempfile.NamedTemporaryFile(prefix=prefix, suffix=suffix, delete=False) as tmp_file:
         tmp_file_name = tmp_file.name
     return tmp_file_name
 
diff --git a/pyproject.toml b/pyproject.toml
index 972b91b36..1b447ce94 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b6"  # TODO: To become 8.8.5
+version = "8.8.4.1b7"  # 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"

From d932bba090e1a2d504f92c6ad1f25f9a6b20a61b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 25 Apr 2024 07:26:07 -0400
Subject: [PATCH 12/46] added are_files_equal to file_utils

---
 CHANGELOG.rst           |  2 +-
 dcicutils/file_utils.py | 20 ++++++++++++++++++++
 pyproject.toml          |  2 +-
 3 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 0306c7cf5..9a4b538f3 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -18,7 +18,7 @@ Change Log
   - Added extract_file_from_zip to zip_utils.
   - Added http_utils with download function.
   - Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
-  - Added normalize_file_path to file_utils.
+  - Added normalize_file_path and are_files_equal to file_utils.
   - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
 
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 987595636..1cd62da6f 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -76,3 +76,23 @@ def normalize_file_path(path: str, home_directory: bool = True) -> str:
         if path.startswith(home_directory) and path != home_directory:
             path = "~/" + pathlib.Path(path).relative_to(home_directory).as_posix()
     return path
+
+
+def are_files_equal(filea: str, fileb: str) -> bool:
+    """
+    Returns True iff the contents of the two given files are exactly the same.
+    """
+    try:
+        with open(filea, "rb") as fa:
+            with open(fileb, "rb") as fb:
+                chunk_size = 4096
+                while True:
+                    chunka = fa.read(chunk_size)
+                    chunkb = fb.read(chunk_size)
+                    if chunka != chunkb:
+                        return False
+                    if not chunka:
+                        break
+        return True
+    except Exception:
+        return False
diff --git a/pyproject.toml b/pyproject.toml
index 1b447ce94..70517487e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b7"  # TODO: To become 8.8.5
+version = "8.8.4.1b8"  # 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"

From d11005445032f01a48963ecae260284797ac704b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 25 Apr 2024 09:01:15 -0400
Subject: [PATCH 13/46] added are_files_equal to file_utils

---
 CHANGELOG.rst           |  2 +-
 dcicutils/file_utils.py | 16 ++++++++++++++++
 pyproject.toml          |  2 +-
 3 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 9a4b538f3..4d4271604 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -18,7 +18,7 @@ Change Log
   - Added extract_file_from_zip to zip_utils.
   - Added http_utils with download function.
   - Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
-  - Added normalize_file_path and are_files_equal to file_utils.
+  - Added normalize_file_path, are_files_equal, and create_random_file to file_utils.
   - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
 
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 1cd62da6f..a1bd0def5 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -1,7 +1,10 @@
 import glob
 import os
 import pathlib
+import random
+import string
 from typing import List, Optional, Union
+from dcicutils.tmpfile_utils import create_temporary_file_name
 
 
 def search_for_file(file: str,
@@ -96,3 +99,16 @@ def are_files_equal(filea: str, fileb: str) -> bool:
         return True
     except Exception:
         return False
+
+
+def create_random_file(file: Optional[str] = None,
+                       prefix: Optional[str] = None, suffix: Optional[str] = None,
+                       nbytes: int = 1024, binary: bool = False) -> str:
+    if not file:
+        file = create_temporary_file_name(prefix=prefix, suffix=suffix)
+    with open(file, "wb" if binary is True else "w") as f:
+        if binary is True:
+            f.write(os.urandom(nbytes))
+        else:
+            f.write(''.join(random.choices(string.ascii_letters + string.digits, k=nbytes)))
+    return file
diff --git a/pyproject.toml b/pyproject.toml
index 70517487e..65a60a7e6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b8"  # TODO: To become 8.8.5
+version = "8.8.4.1b9"  # 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"

From 556f60b8aa6275bbc2ebb09cac44605ab0165995 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 25 Apr 2024 10:06:40 -0400
Subject: [PATCH 14/46] added are_files_equal to file_utils

---
 dcicutils/file_utils.py | 19 +++++++++++++++++--
 pyproject.toml          |  2 +-
 2 files changed, 18 insertions(+), 3 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index a1bd0def5..eb865fd64 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -104,11 +104,26 @@ def are_files_equal(filea: str, fileb: str) -> bool:
 def create_random_file(file: Optional[str] = None,
                        prefix: Optional[str] = None, suffix: Optional[str] = None,
                        nbytes: int = 1024, binary: bool = False) -> str:
-    if not file:
+    if not isinstance(nbytes, int) or nbytes < 0:
+        nbytes = 0
+    if not isinstance(file, str) or not file:
+        if not isinstance(prefix, str):
+            prefix = ""
+        if not isinstance(suffix, str):
+            suffix = ""
         file = create_temporary_file_name(prefix=prefix, suffix=suffix)
     with open(file, "wb" if binary is True else "w") as f:
         if binary is True:
             f.write(os.urandom(nbytes))
         else:
-            f.write(''.join(random.choices(string.ascii_letters + string.digits, k=nbytes)))
+            nchars = 81
+            nlines = nbytes // nchars
+            nremainder = nbytes % nchars
+            for n in range(nlines):
+                f.write("".join(random.choices(string.ascii_letters + string.digits, k=nchars - 1)))
+                f.write("\n")
+            if nremainder > 1:
+                f.write("".join(random.choices(string.ascii_letters + string.digits, k=nremainder - 1)))
+            if nremainder > 0:
+                f.write("\n")
     return file
diff --git a/pyproject.toml b/pyproject.toml
index 65a60a7e6..b335f35d0 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b9"  # TODO: To become 8.8.5
+version = "8.8.4.1b10"  # 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"

From 0f05f120b6157e649eb5e9c94d049e99a1eb29f1 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 25 Apr 2024 12:58:42 -0400
Subject: [PATCH 15/46] version

---
 dcicutils/file_utils.py | 12 +++++++-----
 pyproject.toml          |  2 +-
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index eb865fd64..89c4af368 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -103,7 +103,7 @@ def are_files_equal(filea: str, fileb: str) -> bool:
 
 def create_random_file(file: Optional[str] = None,
                        prefix: Optional[str] = None, suffix: Optional[str] = None,
-                       nbytes: int = 1024, binary: bool = False) -> str:
+                       nbytes: int = 1024, binary: bool = False, line_length: Optional[int] = None) -> str:
     if not isinstance(nbytes, int) or nbytes < 0:
         nbytes = 0
     if not isinstance(file, str) or not file:
@@ -116,11 +116,13 @@ def create_random_file(file: Optional[str] = None,
         if binary is True:
             f.write(os.urandom(nbytes))
         else:
-            nchars = 81
-            nlines = nbytes // nchars
-            nremainder = nbytes % nchars
+            if (not isinstance(line_length, int)) or (line_length < 1):
+                line_length = 80
+            line_length += 1
+            nlines = nbytes // line_length
+            nremainder = nbytes % line_length
             for n in range(nlines):
-                f.write("".join(random.choices(string.ascii_letters + string.digits, k=nchars - 1)))
+                f.write("".join(random.choices(string.ascii_letters + string.digits, k=line_length - 1)))
                 f.write("\n")
             if nremainder > 1:
                 f.write("".join(random.choices(string.ascii_letters + string.digits, k=nremainder - 1)))
diff --git a/pyproject.toml b/pyproject.toml
index b335f35d0..4e4617f0c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b10"  # TODO: To become 8.8.5
+version = "8.8.4.1b11"  # 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"

From 16af8a70f2eaadfa3f2b97f18f6635ab5590d795 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 26 Apr 2024 20:24:36 -0400
Subject: [PATCH 16/46] minor file_utils updates

---
 dcicutils/file_utils.py    |  7 +++++--
 dcicutils/tmpfile_utils.py | 29 ++++++++++++++++++++---------
 pyproject.toml             |  2 +-
 3 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 89c4af368..2fce90fb2 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -1,10 +1,12 @@
 import glob
 import os
 import pathlib
+from datetime import datetime
 import random
 import string
+from tempfile import gettempdir as get_temporary_directory
 from typing import List, Optional, Union
-from dcicutils.tmpfile_utils import create_temporary_file_name
+from uuid import uuid4 as uuid
 
 
 def search_for_file(file: str,
@@ -111,7 +113,8 @@ def create_random_file(file: Optional[str] = None,
             prefix = ""
         if not isinstance(suffix, str):
             suffix = ""
-        file = create_temporary_file_name(prefix=prefix, suffix=suffix)
+        file = f"{datetime.utcnow().strftime('%Y%m%d%H%M%S')}{str(uuid()).replace('-', '')}"
+        file = os.path.join(get_temporary_directory(), file)
     with open(file, "wb" if binary is True else "w") as f:
         if binary is True:
             f.write(os.urandom(nbytes))
diff --git a/dcicutils/tmpfile_utils.py b/dcicutils/tmpfile_utils.py
index 68303da92..dd0c6ac7b 100644
--- a/dcicutils/tmpfile_utils.py
+++ b/dcicutils/tmpfile_utils.py
@@ -1,8 +1,11 @@
 from contextlib import contextmanager
+from datetime import datetime
 import os
 import shutil
 import tempfile
+from uuid import uuid4 as uuid
 from typing import List, Optional, Union
+from dcicutils.file_utils import create_random_file
 
 
 @contextmanager
@@ -25,6 +28,23 @@ def temporary_file(name: Optional[str] = None, suffix: Optional[str] = None,
         yield tmp_file_name
 
 
+def create_temporary_file_name(prefix: Optional[str] = None, suffix: Optional[str] = None) -> str:
+    """
+    Generates and returns the full path to file within the system temporary directory.
+    """
+    tmp_file_name = f"{datetime.utcnow().strftime('%Y%m%d%H%M%S')}{str(uuid()).replace('-', '')}"
+    return os.path.join(tempfile.gettempdir(), tmp_file_name)
+
+
+@contextmanager
+def temporary_random_file(prefix: Optional[str] = None, suffix: Optional[str] = None,
+                          nbytes: int = 1024, binary: bool = False, line_length: Optional[int] = None) -> str:
+    with temporary_file() as tmp_file_path:
+        create_random_file(tmp_file_path, prefix=prefix, suffix=suffix,
+                           nbytes=nbytes, binary=binary, line_length=line_length)
+        yield tmp_file_path
+
+
 def remove_temporary_directory(tmp_directory_name: str) -> None:
     """
     Removes the given directory, recursively; but ONLY if it is (somewhere) within the system temporary directory.
@@ -39,15 +59,6 @@ def is_temporary_directory(path: str) -> bool:
         shutil.rmtree(tmp_directory_name)
 
 
-def create_temporary_file_name(prefix: Optional[str] = None, suffix: Optional[str] = None) -> str:
-    """
-    Generates and returns the full path to file within the system temporary directory.
-    """
-    with tempfile.NamedTemporaryFile(prefix=prefix, suffix=suffix, delete=False) as tmp_file:
-        tmp_file_name = tmp_file.name
-    return tmp_file_name
-
-
 def remove_temporary_file(tmp_file_name: str) -> bool:
     """
     Removes the given file; but ONLY if it is (somewhere) within the system temporary directory.
diff --git a/pyproject.toml b/pyproject.toml
index 4e4617f0c..a0a773ce8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b11"  # TODO: To become 8.8.5
+version = "8.8.4.1b12"  # 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"

From 97a67da0ccbdef811882f170cd2eff6500616ed5 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 26 Apr 2024 23:31:22 -0400
Subject: [PATCH 17/46] minor tmpfile_utils fixes

---
 dcicutils/file_utils.py    | 10 ++++++++--
 dcicutils/tmpfile_utils.py | 17 +++++++++--------
 pyproject.toml             |  2 +-
 3 files changed, 18 insertions(+), 11 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 2fce90fb2..f6dbbc918 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -103,9 +103,15 @@ def are_files_equal(filea: str, fileb: str) -> bool:
         return False
 
 
-def create_random_file(file: Optional[str] = None,
-                       prefix: Optional[str] = None, suffix: Optional[str] = None,
+def create_random_file(file: Optional[str] = None, prefix: Optional[str] = None, suffix: Optional[str] = None,
                        nbytes: int = 1024, binary: bool = False, line_length: Optional[int] = None) -> str:
+    """
+    Write to the given file (name/path) some random content. If the given file is None then writes
+    to a temporary file. In either case, returns the file written to. The of bytes written is 1024
+    by default be can be specified with the nbytes argument; default to writing ASCII text but if
+    the binary argument is True then writes binary data as well; if not binary the content is in
+    lines of 80 characters each; use the line_length argumetn in this case to change the line length.
+    """
     if not isinstance(nbytes, int) or nbytes < 0:
         nbytes = 0
     if not isinstance(file, str) or not file:
diff --git a/dcicutils/tmpfile_utils.py b/dcicutils/tmpfile_utils.py
index dd0c6ac7b..6256f3fbd 100644
--- a/dcicutils/tmpfile_utils.py
+++ b/dcicutils/tmpfile_utils.py
@@ -18,30 +18,31 @@ def temporary_directory() -> str:
 
 
 @contextmanager
-def temporary_file(name: Optional[str] = None, suffix: Optional[str] = None,
+def temporary_file(name: Optional[str] = None, prefix: Optional[str] = None, suffix: Optional[str] = None,
                    content: Optional[Union[str, bytes, List[str]]] = None) -> str:
     with temporary_directory() as tmp_directory_name:
-        tmp_file_name = os.path.join(tmp_directory_name, name or tempfile.mktemp(dir="")) + (suffix or "")
-        with open(tmp_file_name, "wb" if isinstance(content, bytes) else "w") as tmp_file:
+        tmp_file_name = f"{prefix or ''}{name or tempfile.mktemp(dir='')}{suffix or ''}"
+        tmp_file_path = os.path.join(tmp_directory_name, tmp_file_name)
+        with open(tmp_file_path, "wb" if isinstance(content, bytes) else "w") as tmp_file:
             if content is not None:
                 tmp_file.write("\n".join(content) if isinstance(content, list) else content)
-        yield tmp_file_name
+        yield tmp_file_path
 
 
 def create_temporary_file_name(prefix: Optional[str] = None, suffix: Optional[str] = None) -> str:
     """
     Generates and returns the full path to file within the system temporary directory.
     """
-    tmp_file_name = f"{datetime.utcnow().strftime('%Y%m%d%H%M%S')}{str(uuid()).replace('-', '')}"
+    random_string = f"{datetime.utcnow().strftime('%Y%m%d%H%M%S')}{str(uuid()).replace('-', '')}"
+    tmp_file_name = f"{prefix or ''}{random_string}{suffix or ''}"
     return os.path.join(tempfile.gettempdir(), tmp_file_name)
 
 
 @contextmanager
 def temporary_random_file(prefix: Optional[str] = None, suffix: Optional[str] = None,
                           nbytes: int = 1024, binary: bool = False, line_length: Optional[int] = None) -> str:
-    with temporary_file() as tmp_file_path:
-        create_random_file(tmp_file_path, prefix=prefix, suffix=suffix,
-                           nbytes=nbytes, binary=binary, line_length=line_length)
+    with temporary_file(prefix=prefix, suffix=suffix) as tmp_file_path:
+        create_random_file(tmp_file_path, nbytes=nbytes, binary=binary, line_length=line_length)
         yield tmp_file_path
 
 
diff --git a/pyproject.toml b/pyproject.toml
index a0a773ce8..04c61660e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b12"  # TODO: To become 8.8.5
+version = "8.8.4.1b13"  # 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"

From 2004f6626ad6af47d7c9177721223d9c4cca4bd3 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Mon, 29 Apr 2024 09:56:43 -0400
Subject: [PATCH 18/46] added short_uuid to misc_utils

---
 CHANGELOG.rst           |  2 +-
 dcicutils/misc_utils.py |  7 +++++++
 poetry.lock             | 43 ++++++++++++++++++++++++++---------------
 pyproject.toml          | 11 ++++++-----
 4 files changed, 41 insertions(+), 22 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 4d4271604..fede69185 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -17,7 +17,7 @@ Change Log
 * Few general things initially related to rclone support in smaht-submitr:
   - Added extract_file_from_zip to zip_utils.
   - Added http_utils with download function.
-  - Added get_app_specific_directory, get_os_name, and get_cpu_architecture_name to misc_utils.
+  - Added get_app_specific_directory, get_os_name, get_cpu_architecture_name, short_uuid to misc_utils.
   - Added normalize_file_path, are_files_equal, and create_random_file to file_utils.
   - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 34b8fc320..99366570a 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -19,6 +19,7 @@
 import re
 import rfc3986.validators
 import rfc3986.exceptions
+import shortuuid
 import time
 import uuid
 import warnings
@@ -2698,3 +2699,9 @@ def get_cpu_architecture_name() -> str:
         if os_architecture_name == "x86_64": return "amd64"  # noqa
         return os_architecture_name
     return ""
+
+
+def short_uuid(length: Optional[int] = None):
+    if (length is None) or (not isinstance(length, int)) or (length < 1):
+        length = 16
+    return shortuuid.ShortUUID().random(length=length)
diff --git a/poetry.lock b/poetry.lock
index fb8013b34..66c5b4352 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -78,17 +78,17 @@ lxml = ["lxml"]
 
 [[package]]
 name = "boto3"
-version = "1.34.90"
+version = "1.34.93"
 description = "The AWS SDK for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "boto3-1.34.90-py3-none-any.whl", hash = "sha256:b2e5cb5b95efcc881e25a3bc872d7a24e75ff4e76f368138e4baf7b9d6ee3422"},
-    {file = "boto3-1.34.90.tar.gz", hash = "sha256:2824e3dd18743ca50e5b10439d20e74647b1416e8a94509cb30beac92d27a18d"},
+    {file = "boto3-1.34.93-py3-none-any.whl", hash = "sha256:b59355bf4a1408563969526f314611dbeacc151cf90ecb22af295dcc4fe18def"},
+    {file = "boto3-1.34.93.tar.gz", hash = "sha256:e39516e4ca21612932599819662759c04485d53ca457996a913163da11f052a4"},
 ]
 
 [package.dependencies]
-botocore = ">=1.34.90,<1.35.0"
+botocore = ">=1.34.93,<1.35.0"
 jmespath = ">=0.7.1,<2.0.0"
 s3transfer = ">=0.10.0,<0.11.0"
 
@@ -97,13 +97,13 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"]
 
 [[package]]
 name = "boto3-stubs"
-version = "1.34.90"
-description = "Type annotations for boto3 1.34.90 generated with mypy-boto3-builder 7.23.2"
+version = "1.34.93"
+description = "Type annotations for boto3 1.34.93 generated with mypy-boto3-builder 7.24.0"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "boto3_stubs-1.34.90-py3-none-any.whl", hash = "sha256:7361f162523168ddcfb3e0cc70e5208e78f95b9f1f2553032036a2b67ab33355"},
-    {file = "boto3_stubs-1.34.90.tar.gz", hash = "sha256:c82f3db8558e28f766361ba1eea7c77dff735f72fef2a0b9dffaa9c0d9ae76a3"},
+    {file = "boto3_stubs-1.34.93-py3-none-any.whl", hash = "sha256:13c86a8137e969cea21a0f5700c66eb74f864cba8b94a816ee66b4224234f645"},
+    {file = "boto3_stubs-1.34.93.tar.gz", hash = "sha256:1aae0f06c56c8d9a67c45afaf61f2e7bc3fefac207ba5946a23b562d2631d8a3"},
 ]
 
 [package.dependencies]
@@ -154,7 +154,7 @@ bedrock-agent = ["mypy-boto3-bedrock-agent (>=1.34.0,<1.35.0)"]
 bedrock-agent-runtime = ["mypy-boto3-bedrock-agent-runtime (>=1.34.0,<1.35.0)"]
 bedrock-runtime = ["mypy-boto3-bedrock-runtime (>=1.34.0,<1.35.0)"]
 billingconductor = ["mypy-boto3-billingconductor (>=1.34.0,<1.35.0)"]
-boto3 = ["boto3 (==1.34.90)", "botocore (==1.34.90)"]
+boto3 = ["boto3 (==1.34.93)", "botocore (==1.34.93)"]
 braket = ["mypy-boto3-braket (>=1.34.0,<1.35.0)"]
 budgets = ["mypy-boto3-budgets (>=1.34.0,<1.35.0)"]
 ce = ["mypy-boto3-ce (>=1.34.0,<1.35.0)"]
@@ -501,13 +501,13 @@ xray = ["mypy-boto3-xray (>=1.34.0,<1.35.0)"]
 
 [[package]]
 name = "botocore"
-version = "1.34.90"
+version = "1.34.93"
 description = "Low-level, data-driven core of boto 3."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "botocore-1.34.90-py3-none-any.whl", hash = "sha256:d48f152498e2c60b43ce25b579d26642346a327b6fb2c632d57219e0a4f63392"},
-    {file = "botocore-1.34.90.tar.gz", hash = "sha256:113cd4c0cb63e13163ccbc2bb13d551be314ba7f8ba5bfab1c51a19ca01aa133"},
+    {file = "botocore-1.34.93-py3-none-any.whl", hash = "sha256:6fbd5a53a2adc9b3d4ebd90ae0ede83a91a41d96231f8a5984051f75495f246d"},
+    {file = "botocore-1.34.93.tar.gz", hash = "sha256:79d39b0b87e962991c6dd55e78ce15155099f6fb741be88b1b8a456a702cc150"},
 ]
 
 [package.dependencies]
@@ -523,13 +523,13 @@ crt = ["awscrt (==0.20.9)"]
 
 [[package]]
 name = "botocore-stubs"
-version = "1.34.90"
+version = "1.34.93"
 description = "Type annotations and code completion for botocore"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "botocore_stubs-1.34.90-py3-none-any.whl", hash = "sha256:0fb0125d3d77a85984dc865f852340d57bc7bedc2efe0ddf56e449da449eeee9"},
-    {file = "botocore_stubs-1.34.90.tar.gz", hash = "sha256:e59dd8576a29639c92d8600edfb412c51fe1742a8ac0b48de637570b220a5f2c"},
+    {file = "botocore_stubs-1.34.93-py3-none-any.whl", hash = "sha256:909ebaf7a70ce83de4d85eed4b810e68c4d4cb64606d7431a263b909c92b7fa4"},
+    {file = "botocore_stubs-1.34.93.tar.gz", hash = "sha256:22e71e4c507df2e91d5673d2b65281c115d4c8d2601a3c2497c7a309fef6a0ec"},
 ]
 
 [package.dependencies]
@@ -1807,6 +1807,17 @@ docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments
 testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
 
+[[package]]
+name = "shortuuid"
+version = "1.0.13"
+description = "A generator library for concise, unambiguous and URL-safe UUIDs."
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "shortuuid-1.0.13-py3-none-any.whl", hash = "sha256:a482a497300b49b4953e15108a7913244e1bb0d41f9d332f5e9925dba33a3c5a"},
+    {file = "shortuuid-1.0.13.tar.gz", hash = "sha256:3bb9cf07f606260584b1df46399c0b87dd84773e7b25912b7e391e30797c5e72"},
+]
+
 [[package]]
 name = "six"
 version = "1.16.0"
@@ -2147,4 +2158,4 @@ testing = ["coverage (>=5.0.3)", "zope.event", "zope.testing"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.8,<3.13"
-content-hash = "3ff0434deeb048d183ca5e6d0ce5d931be4718f18cb6ccebf6250e2edf0aafdb"
+content-hash = "861eae1f51e0ff0fbbb39d9ca2ec5dcb87db5aa6ad730a8f9d92c2507485bba1"
diff --git a/pyproject.toml b/pyproject.toml
index 04c61660e..55921f4cb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b13"  # TODO: To become 8.8.5
+version = "8.8.4.1b15"  # 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"
@@ -38,8 +38,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.8,<3.13"
-boto3 = "^1.34.90"
-botocore = "^1.34.90"
+boto3 = "^1.34.93"
+botocore = "^1.34.93"
 # 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"
@@ -61,6 +61,7 @@ pyperclip = "^1.8.2"
 PyYAML = "^6.0.1"
 requests = "^2.21.0"
 rfc3986 = "^1.4.0"
+shortuuid = "^1.0.13"
 structlog = "^19.2.0"
 toml = ">=0.10.1,<1"
 tqdm = "^4.66.2"
@@ -70,8 +71,8 @@ webtest = "^2.0.34"
 
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.34.90"
-botocore-stubs = "^1.34.90"
+boto3-stubs = "^1.34.93"
+botocore-stubs = "^1.34.93"
 coverage = ">=7.2.3"
 # Loaded manually in GA workflow for coverage because a dependency on 2to3
 # in its docopts dependency makes a problem for laoding it here in poetry. -kmp 7-Apr-2023

From d4f144ea85446e808d69336fda871a26ad2d4510 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 1 May 2024 16:13:02 -0400
Subject: [PATCH 19/46] Added compute_file_md5 and compute_file_etag to
 file_utils.

---
 CHANGELOG.rst           |  1 +
 dcicutils/file_utils.py | 72 +++++++++++++++++++++++++++++++++++++++++
 pyproject.toml          |  2 +-
 3 files changed, 74 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index fede69185..ac289040d 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -20,6 +20,7 @@ Change Log
   - Added get_app_specific_directory, get_os_name, get_cpu_architecture_name, short_uuid to misc_utils.
   - Added normalize_file_path, are_files_equal, and create_random_file to file_utils.
   - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
+  - Added compute_file_md5 and compute_file_etag to file_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
 
 
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index f6dbbc918..22adc32e3 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -1,4 +1,6 @@
 import glob
+import hashlib
+import io
 import os
 import pathlib
 from datetime import datetime
@@ -103,6 +105,76 @@ def are_files_equal(filea: str, fileb: str) -> bool:
         return False
 
 
+def compute_file_md5(file: str) -> str:
+    """
+    Returns the md5 checksum for the given file.
+    """
+    if not isinstance(file, str):
+        return ""
+    try:
+        md5 = hashlib.md5()
+        with open(file, "rb") as file:
+            for chunk in iter(lambda: file.read(4096), b""):
+                md5.update(chunk)
+        return md5.hexdigest()
+    except Exception:
+        return ""
+
+
+def compute_file_etag(file: str) -> Optional[str]:
+    """
+    Returns the AWS S3 "etag" for the given file; this value is md5-like but
+    not the same as a normal md5. We use this to compare that a file in S3
+    appears to be the exact the same file as a local file.
+    """
+    try:
+        with io.open(file, "rb") as f:
+            return _compute_file_etag(f)
+    except Exception:
+        return None
+
+
+def _compute_file_etag(f: io.BufferedReader) -> str:
+    # See: https://stackoverflow.com/questions/75723647/calculate-md5-from-aws-s3-etag
+    MULTIPART_THRESHOLD = 8388608
+    MULTIPART_CHUNKSIZE = 8388608
+    # BUFFER_SIZE = 1048576
+    # Verify some assumptions are correct
+    # assert(MULTIPART_CHUNKSIZE >= MULTIPART_THRESHOLD)
+    # assert((MULTIPART_THRESHOLD % BUFFER_SIZE) == 0)
+    # assert((MULTIPART_CHUNKSIZE % BUFFER_SIZE) == 0)
+    hash = hashlib.md5()
+    read = 0
+    chunks = None
+    while True:
+        # Read some from stdin, if we're at the end, stop reading
+        bits = f.read(1048576)
+        if len(bits) == 0:
+            break
+        read += len(bits)
+        hash.update(bits)
+        if chunks is None:
+            # We're handling a multi-part upload, so switch to calculating
+            # hashes of each chunk
+            if read >= MULTIPART_THRESHOLD:
+                chunks = b''
+        if chunks is not None:
+            if (read % MULTIPART_CHUNKSIZE) == 0:
+                # Dont with a chunk, add it to the list of hashes to hash later
+                chunks += hash.digest()
+                hash = hashlib.md5()
+    if chunks is None:
+        # Normal upload, just output the MD5 hash
+        etag = hash.hexdigest()
+    else:
+        # Multipart upload, need to output the hash of the hashes
+        if (read % MULTIPART_CHUNKSIZE) != 0:
+            # Add the last part if we have a partial chunk
+            chunks += hash.digest()
+        etag = hashlib.md5(chunks).hexdigest() + "-" + str(len(chunks) // 16)
+    return etag
+
+
 def create_random_file(file: Optional[str] = None, prefix: Optional[str] = None, suffix: Optional[str] = None,
                        nbytes: int = 1024, binary: bool = False, line_length: Optional[int] = None) -> str:
     """
diff --git a/pyproject.toml b/pyproject.toml
index 55921f4cb..093017ff3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b15"  # TODO: To become 8.8.5
+version = "8.8.4.1b16"  # 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"

From 71b93ba36ad1100ad8b1a2d80da0c3b156f3f3b5 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 2 May 2024 16:05:05 -0400
Subject: [PATCH 20/46] Added compute_file_md5 and compute_file_etag to
 file_utils.

---
 dcicutils/http_utils.py | 15 +++++++++++++--
 pyproject.toml          |  2 +-
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/dcicutils/http_utils.py b/dcicutils/http_utils.py
index 305d2207d..9ccf743c5 100644
--- a/dcicutils/http_utils.py
+++ b/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
diff --git a/pyproject.toml b/pyproject.toml
index 093017ff3..31f37bd8f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b16"  # TODO: To become 8.8.5
+version = "8.8.4.1b17"  # 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"

From 5db8874b42b1cdf7fd437adac1b536b97ded6636 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 3 May 2024 12:43:51 -0400
Subject: [PATCH 21/46] some minor refactor in search_for_file in file_utils.

---
 CHANGELOG.rst           |  1 +
 dcicutils/file_utils.py | 87 +++++++++++++++++++++++------------------
 pyproject.toml          |  2 +-
 3 files changed, 52 insertions(+), 38 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index ac289040d..9148f489a 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -21,6 +21,7 @@ Change Log
   - Added normalize_file_path, are_files_equal, and create_random_file to file_utils.
   - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
   - Added compute_file_md5 and compute_file_etag to file_utils.
+  - Minor extra sanity check to search_for_file in file_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
 
 
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 22adc32e3..42bb32db6 100644
--- a/dcicutils/file_utils.py
+++ b/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:
diff --git a/pyproject.toml b/pyproject.toml
index 31f37bd8f..e614ae1b8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b17"  # TODO: To become 8.8.5
+version = "8.8.4.1b18"  # 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"

From 69e3a0701f8f8405621c34bc148765cf81207190 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 3 May 2024 14:51:18 -0400
Subject: [PATCH 22/46] some minor refactor in search_for_file in file_utils.

---
 dcicutils/file_utils.py | 7 +++----
 pyproject.toml          | 2 +-
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 42bb32db6..9c0b0f7ff 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -44,11 +44,12 @@ def search_for_file(file: str,
             directory = str(directory)
         if not (directory := directory.strip()):
             continue
-        if os.path.isfile(directory):
+        if os.path.isfile(directory := os.path.normpath(directory)):
             # Allow a file; assume its parent directory was intended.
             if not (directory := os.path.dirname(directory)):
                 continue
-        location_pruned.append(directory)
+        if directory not in location_pruned:
+            location_pruned.append(directory)
     location = location_pruned
     for directory in location:
         if os.path.exists(os.path.join(directory, file)):
@@ -59,8 +60,6 @@ def search_for_file(file: str,
                 files_found.append(file_found)
     if recursive is True:
         for directory in location:
-            if not directory:
-                continue
             if not directory.endswith("/**") and not file.startswith("**/"):
                 path = f"{directory}/**/{file}"
             else:
diff --git a/pyproject.toml b/pyproject.toml
index e614ae1b8..fb91671ad 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b18"  # TODO: To become 8.8.5
+version = "8.8.4.1b19"  # 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"

From a0936489b577cce3841ecc8a528564c0f8499860 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 3 May 2024 14:57:45 -0400
Subject: [PATCH 23/46] some minor refactor in search_for_file in file_utils.

---
 dcicutils/file_utils.py | 2 +-
 pyproject.toml          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 9c0b0f7ff..b1dc7f4f4 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -44,7 +44,7 @@ def search_for_file(file: str,
             directory = str(directory)
         if not (directory := directory.strip()):
             continue
-        if os.path.isfile(directory := os.path.normpath(directory)):
+        if os.path.isfile(directory := os.path.abspath(os.path.normpath(directory))):
             # Allow a file; assume its parent directory was intended.
             if not (directory := os.path.dirname(directory)):
                 continue
diff --git a/pyproject.toml b/pyproject.toml
index fb91671ad..aacb8475a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b19"  # TODO: To become 8.8.5
+version = "8.8.4.1b20"  # 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"

From 37062f18c160a5af45d16d14b751c1d2f2a6084b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Sat, 4 May 2024 11:16:50 -0400
Subject: [PATCH 24/46] factor few misc functions from smaht-submitr to her

---
 CHANGELOG.rst           |  8 +++----
 dcicutils/file_utils.py | 53 ++++++++++++++++++++++++++++-------------
 dcicutils/misc_utils.py | 13 ++++++++++
 3 files changed, 54 insertions(+), 20 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 9148f489a..f7ccc098a 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -14,14 +14,14 @@ Change Log
   for running Foursight checks locally (with local ssh tunnel to ES proxy);
   came up in foursight/checks/audit_checks (2024-04-23).
 * Allow Python 3.12 (pyproject.toml).
-* Few general things initially related to rclone support in smaht-submitr:
+* Few general things initially related to and factored out of rclone support in smaht-submitr:
   - Added extract_file_from_zip to zip_utils.
   - Added http_utils with download function.
   - Added get_app_specific_directory, get_os_name, get_cpu_architecture_name, short_uuid to misc_utils.
-  - Added normalize_file_path, are_files_equal, and create_random_file to file_utils.
-  - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
-  - Added compute_file_md5 and compute_file_etag to file_utils.
+  - Added are_files_equal, create_random_file to file_utils,  compute_file_md5, compute_file_etag,
+    normalize_path, get_file_size, get_file_modified_datetime to file_utils.
   - Minor extra sanity check to search_for_file in file_utils.
+  - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
 
 
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index b1dc7f4f4..02f3847af 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -10,6 +10,8 @@
 from typing import List, Optional, Union
 from uuid import uuid4 as uuid
 
+HOME_DIRECTORY = str(pathlib.Path().home())
+
 
 def search_for_file(file: str,
                     location: Union[str, Optional[List[str]]] = None,
@@ -77,24 +79,43 @@ def search_for_file(file: str,
     return None if single is True else []
 
 
-def normalize_file_path(path: str, home_directory: bool = True) -> str:
+def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, home: Optional[bool] = None) -> str:
     """
-    Normalizes the given file path name and returns. Does things like remove multiple
-    consecutive slashes and redundant/unnecessary parent paths; if the home_directory
-    argument is True (the default) then also handles the special tilde home directory
-    component/convention and uses this in the result if applicable.
+    Normalizes the given path value and returns the result; does things like remove redundant
+    consecutive directory separators and redundant parent paths. If the given absolute argument
+    is True than converts the path to an absolute path. If the given home argument is True and
+    if the path can reasonably be represented with a home directory indicator (i.e. "~"), then
+    converts it to such. If the home argument is False and path starts with the home directory
+    indicator then expands it to the actual (absolute) home path. If the given value is not
+    actually even a string (or pathlib.Path) then returns an empty string.
     """
-    if not isinstance(path, str) or not path:
-        path = os.getcwd()
-    path = os.path.normpath(path)
-    home_directory = os.path.expanduser("~") if home_directory is True else None
-    if home_directory and path.startswith("~"):
-        path = os.path.join(home_directory, path[2 if path.startswith("~/") else 1:])
-    path = os.path.abspath(path)
-    if home_directory and (os.name == "posix"):
-        if path.startswith(home_directory) and path != home_directory:
-            path = "~/" + pathlib.Path(path).relative_to(home_directory).as_posix()
-    return path
+    if isinstance(value, pathlib.Path):
+        value = str(value)
+    elif not isinstance(value, str):
+        return ""
+    if not (value := value.strip()) or not (value := os.path.normpath(value)):
+        return ""
+    if home is False:
+        value = os.path.expanduser(value)
+    elif (home is True) and (os.name == "posix") and value.startswith(home := HOME_DIRECTORY + os.sep):
+        value = "~/" + value[len(home):]
+    if absolute is True:
+        value = os.path.abspath(value)
+    return value
+
+
+def get_file_size(file: str) -> Optional[int]:
+    try:
+        return os.path.getsize(file) if isinstance(file, str) else None
+    except Exception:
+        return None
+
+
+def get_file_modified_datetime(file: str) -> Optional[datetime]:
+    try:
+        return datetime.fromtimestamp(os.path.getmtime(file)) if isinstance(file, str) else None
+    except Exception:
+        return None
 
 
 def are_files_equal(filea: str, fileb: str) -> bool:
diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 99366570a..249524d6c 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -2551,6 +2551,19 @@ def normalize_spaces(value: str) -> str:
     return re.sub(r"\s+", " ", value).strip()
 
 
+def normalize_string(value: Optional[str]) -> Optional[str]:
+    """
+    Strips leading/trailing spaces, and converts multiple consecutive spaces to a single space
+    in the given string value and returns the result. If the given value is None returns an
+    empty string. If the given value is not actually even a string then return None.
+    """
+    if value is None:
+        return ""
+    elif isinstance(value, str):
+        return value.strip()
+    return None
+
+
 def find_nth_from_end(string: str, substring: str, nth: int) -> int:
     """
     Returns the index of the nth occurrence of the given substring within

From 59a71d7a37861175b94a7bb58bbfdf9821e49eae Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Sat, 4 May 2024 11:17:02 -0400
Subject: [PATCH 25/46] verison

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index aacb8475a..56622d8fc 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b20"  # TODO: To become 8.8.5
+version = "8.8.4.1b21"  # 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"

From 33e1edfdb693c1a7444113349f1d370bedf5a507 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Mon, 6 May 2024 12:15:29 -0400
Subject: [PATCH 26/46] added create_uuid to misc_utils

---
 dcicutils/misc_utils.py | 17 +++++++++++++++--
 pyproject.toml          |  2 +-
 2 files changed, 16 insertions(+), 3 deletions(-)

diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 249524d6c..1ffab1607 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -2714,7 +2714,20 @@ def get_cpu_architecture_name() -> str:
     return ""
 
 
-def short_uuid(length: Optional[int] = None):
+def create_uuid(nodash: bool = False, upper: bool = False) -> str:
+    value = str(uuid.uuid4())
+    if nodash is True:
+        value = value.replace("-", "")
+    if upper is True:
+        value = value.upper()
+    return value
+
+
+def create_short_uuid(length: Optional[int] = None, upper: bool = False):
+    # Not really techincally a uuid of course.
     if (length is None) or (not isinstance(length, int)) or (length < 1):
         length = 16
-    return shortuuid.ShortUUID().random(length=length)
+    value = shortuuid.ShortUUID().random(length=length)
+    if upper is True:
+        value = value.upper()
+    return value
diff --git a/pyproject.toml b/pyproject.toml
index 56622d8fc..a9e289f9b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b21"  # TODO: To become 8.8.5
+version = "8.8.4.1b22"  # 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"

From 09d6f2fdc1ae33a003239e67c9aa99959324ae3b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Mon, 6 May 2024 16:07:24 -0400
Subject: [PATCH 27/46] tests for file_utils.normalize_path

---
 dcicutils/file_utils.py | 16 +++++++--------
 pyproject.toml          |  2 +-
 test/test_file_utils.py | 43 ++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 51 insertions(+), 10 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 02f3847af..60c62f1ac 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -79,15 +79,15 @@ def search_for_file(file: str,
     return None if single is True else []
 
 
-def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, home: Optional[bool] = None) -> str:
+def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, expand_home: Optional[bool] = None) -> str:
     """
     Normalizes the given path value and returns the result; does things like remove redundant
     consecutive directory separators and redundant parent paths. If the given absolute argument
-    is True than converts the path to an absolute path. If the given home argument is True and
-    if the path can reasonably be represented with a home directory indicator (i.e. "~"), then
-    converts it to such. If the home argument is False and path starts with the home directory
-    indicator then expands it to the actual (absolute) home path. If the given value is not
-    actually even a string (or pathlib.Path) then returns an empty string.
+    is True than converts the path to an absolute path. If the given expand_home argument is False
+    and if the path can reasonably be represented with a home directory indicator (i.e. "~"), then
+    converts it to such. If the expand_home argument is True and path starts with the home directory
+    indicator (i.e. "~") then expands it to the actual (absolute) home path of the caller. If the
+    given path value is not actually even a string (or pathlib.Path) then returns an empty string.
     """
     if isinstance(value, pathlib.Path):
         value = str(value)
@@ -95,9 +95,9 @@ def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, home
         return ""
     if not (value := value.strip()) or not (value := os.path.normpath(value)):
         return ""
-    if home is False:
+    if expand_home is True:
         value = os.path.expanduser(value)
-    elif (home is True) and (os.name == "posix") and value.startswith(home := HOME_DIRECTORY + os.sep):
+    elif (expand_home is False) and (os.name == "posix") and value.startswith(home := HOME_DIRECTORY + os.sep):
         value = "~/" + value[len(home):]
     if absolute is True:
         value = os.path.abspath(value)
diff --git a/pyproject.toml b/pyproject.toml
index a9e289f9b..fc4e8d053 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b22"  # TODO: To become 8.8.5
+version = "8.8.4.1b23"  # 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"
diff --git a/test/test_file_utils.py b/test/test_file_utils.py
index d27477469..d1f618a09 100644
--- a/test/test_file_utils.py
+++ b/test/test_file_utils.py
@@ -1,7 +1,22 @@
+import importlib
+import pytest
 import os
-from dcicutils.file_utils import search_for_file
+from dcicutils.file_utils import normalize_path, search_for_file
 from dcicutils.tmpfile_utils import temporary_directory
 
+HOME_DIRECTORY = "/Some/HomeDirectory"
+CURRENT_DIRECTORY = os.path.abspath(os.path.curdir)
+
+
+@pytest.fixture(autouse=True)
+def monkey_path_home_directory(monkeypatch):
+    monkeypatch.setenv("HOME", HOME_DIRECTORY)
+    file_utils_module = importlib.import_module("dcicutils.file_utils")
+    save_home_directory = file_utils_module.HOME_DIRECTORY
+    file_utils_module.HOME_DIRECTORY = HOME_DIRECTORY
+    yield
+    file_utils_module = save_home_directory
+
 
 def test_search_for_file():
 
@@ -38,3 +53,29 @@ def test_search_for_file():
                 assert (set(search_for_file(filename, location=topdirname, recursive=True)) ==
                         set([filepath, subfilepath]))
                 assert search_for_file(filename, location=topdirname, recursive=False) == []
+
+
+def test_normalize_path():
+    assert os.environ["HOME"] == HOME_DIRECTORY
+    assert normalize_path(None) == ""
+    assert normalize_path("") == ""
+    assert normalize_path(123) == ""
+    assert normalize_path("///") == "/"
+    assert normalize_path(".") == "."
+    assert normalize_path(".//") == "."
+    assert normalize_path("/") == "/"
+    assert normalize_path("/.") == "/"
+    assert normalize_path("./abc") == "abc"
+    assert normalize_path("./abc", absolute=True) == f"{CURRENT_DIRECTORY}/abc"
+    assert normalize_path("/abc/def") == "/abc/def"
+    assert normalize_path("/abc/def/") == "/abc/def"
+    assert normalize_path("/abc///def") == "/abc/def"
+    assert normalize_path("///abc///def") == "/abc/def"
+    assert normalize_path("~///Ghi//Jkl//") == "~/Ghi/Jkl"
+    assert normalize_path("~///Ghi//Jkl/", expand_home=False, absolute=False) == "~/Ghi/Jkl"
+    assert normalize_path("~///Ghi//Jkl/", absolute=True) == f"{CURRENT_DIRECTORY}/~/Ghi/Jkl"
+    assert normalize_path("~///Ghi//Jkl/", expand_home=True, absolute=True) == f"{HOME_DIRECTORY}/Ghi/Jkl"
+    assert normalize_path("~///Ghi//Jkl/", expand_home=True, absolute=False) == f"{HOME_DIRECTORY}/Ghi/Jkl"
+    assert normalize_path("~///Ghi//Jkl/", expand_home=False, absolute=True) == f"{CURRENT_DIRECTORY}/~/Ghi/Jkl"
+    assert normalize_path("~///Ghi//Jkl/", expand_home=True) == f"{HOME_DIRECTORY}/Ghi/Jkl"
+    assert normalize_path(f"{HOME_DIRECTORY}/Ghi//Jkl/", expand_home=False) == "~/Ghi/Jkl"

From 12456fbdcd296189ed8bb78c3a9d1464e54f661a Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Mon, 6 May 2024 16:15:32 -0400
Subject: [PATCH 28/46] version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index fc4e8d053..2cc997a12 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b23"  # TODO: To become 8.8.5
+version = "8.8.4.1b24"  # 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"

From a5dee767d1d67f604956c9b66e3dcd1773e674d6 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Mon, 6 May 2024 16:31:25 -0400
Subject: [PATCH 29/46] minor updates from pr-305 feedback

---
 dcicutils/file_utils.py | 20 ++++++++++++++-----
 dcicutils/http_utils.py | 44 ++++++++++++++++++++++++-----------------
 pyproject.toml          |  2 +-
 3 files changed, 42 insertions(+), 24 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 60c62f1ac..defad2da5 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -104,21 +104,25 @@ def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, expa
     return value
 
 
-def get_file_size(file: str) -> Optional[int]:
+def get_file_size(file: str, raise_exception: bool = True) -> Optional[int]:
     try:
         return os.path.getsize(file) if isinstance(file, str) else None
     except Exception:
+        if raise_exception is True:
+            raise
         return None
 
 
-def get_file_modified_datetime(file: str) -> Optional[datetime]:
+def get_file_modified_datetime(file: str, raise_exception: bool = True) -> Optional[datetime]:
     try:
         return datetime.fromtimestamp(os.path.getmtime(file)) if isinstance(file, str) else None
     except Exception:
+        if raise_exception is True:
+            raise
         return None
 
 
-def are_files_equal(filea: str, fileb: str) -> bool:
+def are_files_equal(filea: str, fileb: str, raise_exception: bool = True) -> bool:
     """
     Returns True iff the contents of the two given files are exactly the same.
     """
@@ -135,10 +139,12 @@ def are_files_equal(filea: str, fileb: str) -> bool:
                         break
         return True
     except Exception:
+        if raise_exception is True:
+            raise
         return False
 
 
-def compute_file_md5(file: str) -> str:
+def compute_file_md5(file: str, raise_exception: bool = True) -> str:
     """
     Returns the md5 checksum for the given file.
     """
@@ -151,10 +157,12 @@ def compute_file_md5(file: str) -> str:
                 md5.update(chunk)
         return md5.hexdigest()
     except Exception:
+        if raise_exception is True:
+            raise
         return ""
 
 
-def compute_file_etag(file: str) -> Optional[str]:
+def compute_file_etag(file: str, raise_exception: bool = True) -> Optional[str]:
     """
     Returns the AWS S3 "etag" for the given file; this value is md5-like but
     not the same as a normal md5. We use this to compare that a file in S3
@@ -164,6 +172,8 @@ def compute_file_etag(file: str) -> Optional[str]:
         with io.open(file, "rb") as f:
             return _compute_file_etag(f)
     except Exception:
+        if raise_exception is True:
+            raise
         return None
 
 
diff --git a/dcicutils/http_utils.py b/dcicutils/http_utils.py
index 9ccf743c5..a82da78bd 100644
--- a/dcicutils/http_utils.py
+++ b/dcicutils/http_utils.py
@@ -8,24 +8,32 @@
 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.
+    Context manager to download the given URL into a temporary file and yields the file
+    path to it. An optional file suffix may be specified for this temporary file name.
+    Defaults to binary file mode; if 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)
+        download_to(url, file, binary=binary, progress=progress)
         yield file
+
+
+def download_to(url: str, file: str, binary: bool = True, progress: Optional[Callable] = None) -> None:
+    """
+    Download the given URL into the given file. Defaults to binary
+    file mode; if not desired then pass False as the binary argument.
+    """
+    if not callable(progress):
+        progress = None
+    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)
diff --git a/pyproject.toml b/pyproject.toml
index 2cc997a12..da8d34ecb 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b24"  # TODO: To become 8.8.5
+version = "8.8.4.1b26"  # 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"

From 3fa91c6639f3944ae72fc336a19d868499d9d575 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 7 May 2024 05:39:08 -0400
Subject: [PATCH 30/46] file_utils tests

---
 dcicutils/file_utils.py | 7 +++++--
 test/test_file_utils.py | 4 ++++
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index defad2da5..8afdbc685 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -97,8 +97,11 @@ def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, expa
         return ""
     if expand_home is True:
         value = os.path.expanduser(value)
-    elif (expand_home is False) and (os.name == "posix") and value.startswith(home := HOME_DIRECTORY + os.sep):
-        value = "~/" + value[len(home):]
+    elif (expand_home is False) and (os.name == "posix"):
+        if value.startswith(home := HOME_DIRECTORY + os.sep):
+            value = "~/" + value[len(home):]
+        elif value == HOME_DIRECTORY:
+            value = "~"
     if absolute is True:
         value = os.path.abspath(value)
     return value
diff --git a/test/test_file_utils.py b/test/test_file_utils.py
index d1f618a09..46700f4dd 100644
--- a/test/test_file_utils.py
+++ b/test/test_file_utils.py
@@ -79,3 +79,7 @@ def test_normalize_path():
     assert normalize_path("~///Ghi//Jkl/", expand_home=False, absolute=True) == f"{CURRENT_DIRECTORY}/~/Ghi/Jkl"
     assert normalize_path("~///Ghi//Jkl/", expand_home=True) == f"{HOME_DIRECTORY}/Ghi/Jkl"
     assert normalize_path(f"{HOME_DIRECTORY}/Ghi//Jkl/", expand_home=False) == "~/Ghi/Jkl"
+    assert normalize_path(f"{HOME_DIRECTORY}", expand_home=False) == "~"
+    assert normalize_path(f"{HOME_DIRECTORY}/", expand_home=False) == "~"
+    assert normalize_path(f"{HOME_DIRECTORY}/.ssh", expand_home=False) == "~/.ssh"
+    assert normalize_path(f"~/.ssh", expand_home=True) == f"{HOME_DIRECTORY}/.ssh"

From 2c866fd241147ffef6297d63e637f3a027a7c50b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 7 May 2024 05:39:21 -0400
Subject: [PATCH 31/46] file_utils tests

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index da8d34ecb..77bd9c31e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b26"  # TODO: To become 8.8.5
+version = "8.8.4.1b27"  # 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"

From 673de268681aacf761013e13e276780532c88282 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 8 May 2024 18:33:27 -0400
Subject: [PATCH 32/46] added ordering to file_utils.search_for_files

---
 CHANGELOG.rst           |  1 +
 dcicutils/file_utils.py | 17 +++++++++++++----
 pyproject.toml          |  2 +-
 3 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index f7ccc098a..507f919d1 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -21,6 +21,7 @@ Change Log
   - Added are_files_equal, create_random_file to file_utils,  compute_file_md5, compute_file_etag,
     normalize_path, get_file_size, get_file_modified_datetime to file_utils.
   - Minor extra sanity check to search_for_file in file_utils.
+  - Added deterministic ordering to paths returned by search_for_file in file_utils.
   - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
 
diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 8afdbc685..552d314ac 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -16,7 +16,8 @@
 def search_for_file(file: str,
                     location: Union[str, Optional[List[str]]] = None,
                     recursive: bool = False,
-                    single: bool = False) -> Union[List[str], Optional[str]]:
+                    single: bool = False,
+                    order: bool = True) -> Union[List[str], Optional[str]]:
     """
     Searches for the existence of the given file name, first directly in the given directory or list
     of directories, if specified, and if not then just in the current (working) directory; if the
@@ -25,6 +26,11 @@ 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.
     """
+    def order_by_fewest_number_of_paths_and_then_alphabetically(paths: List[str]) -> List[str]:
+        def order_by(path: str):
+            return len(path.split(os.path.sep)), path
+        return sorted(paths, key=order_by, reverse=True)
+
     if not (file and isinstance(file, (str, pathlib.PosixPath))):
         return None if single is True else []
     if os.path.isabs(file):
@@ -74,9 +80,12 @@ def search_for_file(file: str,
                         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 []
+    if single is True:
+        return files_found[0] if files_found else None
+    elif order is True:
+        return order_by_fewest_number_of_paths_and_then_alphabetically(files_found)
+    else:
+        return files_found
 
 
 def normalize_path(value: Union[str, pathlib.Path], absolute: bool = False, expand_home: Optional[bool] = None) -> str:
diff --git a/pyproject.toml b/pyproject.toml
index 77bd9c31e..66fed4d25 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b27"  # TODO: To become 8.8.5
+version = "8.8.4.1b28"  # 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"

From 8f78d94df7b578515b24038775d6bd242b27d65c Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 8 May 2024 18:34:01 -0400
Subject: [PATCH 33/46] added ordering to file_utils.search_for_files

---
 dcicutils/file_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 552d314ac..0ebc8e4cd 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -29,7 +29,7 @@ def search_for_file(file: str,
     def order_by_fewest_number_of_paths_and_then_alphabetically(paths: List[str]) -> List[str]:
         def order_by(path: str):
             return len(path.split(os.path.sep)), path
-        return sorted(paths, key=order_by, reverse=True)
+        return sorted(paths, key=order_by)
 
     if not (file and isinstance(file, (str, pathlib.PosixPath))):
         return None if single is True else []

From 71a431878171b00042d13d0f8711c09d065d7010 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Mon, 13 May 2024 10:54:58 -0400
Subject: [PATCH 34/46] minor misc_utils.normalize_string fix

---
 dcicutils/misc_utils.py | 2 +-
 pyproject.toml          | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 1ffab1607..17ba61810 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -2560,7 +2560,7 @@ def normalize_string(value: Optional[str]) -> Optional[str]:
     if value is None:
         return ""
     elif isinstance(value, str):
-        return value.strip()
+        return re.sub(r"\s+", " ", value).strip()
     return None
 
 
diff --git a/pyproject.toml b/pyproject.toml
index 66fed4d25..db663dc95 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b28"  # TODO: To become 8.8.5
+version = "8.8.4.1b30"  # 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"

From f7f2956a29f3eca0b2f0d7e395afdcb52f9d53e0 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 14 May 2024 22:37:44 -0400
Subject: [PATCH 35/46] lint-complaint-misc-utils

---
 dcicutils/misc_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 17ba61810..56e5a0b34 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -2693,7 +2693,7 @@ 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
+    - 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()

From 6203a710d3022e52848a76fe387f201b46732574 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Tue, 14 May 2024 22:37:58 -0400
Subject: [PATCH 36/46] version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index db663dc95..0cd50ccff 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b30"  # TODO: To become 8.8.5
+version = "8.8.4.1b31"  # 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"

From c31227a8f23049a2847c510efbfdd2eaf67df722 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 15 May 2024 10:02:18 -0400
Subject: [PATCH 37/46] made is_temporary_directory top-level function in
 tmpfile_utils

---
 dcicutils/tmpfile_utils.py | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/dcicutils/tmpfile_utils.py b/dcicutils/tmpfile_utils.py
index 6256f3fbd..e944ac46d 100644
--- a/dcicutils/tmpfile_utils.py
+++ b/dcicutils/tmpfile_utils.py
@@ -50,12 +50,6 @@ def remove_temporary_directory(tmp_directory_name: str) -> None:
     """
     Removes the given directory, recursively; but ONLY if it is (somewhere) within the system temporary directory.
     """
-    def is_temporary_directory(path: str) -> bool:
-        try:
-            tmpdir = tempfile.gettempdir()
-            return os.path.commonpath([path, tmpdir]) == tmpdir and os.path.exists(path) and os.path.isdir(path)
-        except Exception:
-            return False
     if is_temporary_directory(tmp_directory_name):  # Guard against errant deletion.
         shutil.rmtree(tmp_directory_name)
 
@@ -72,3 +66,11 @@ def remove_temporary_file(tmp_file_name: str) -> bool:
         return False
     except Exception:
         return False
+
+
+def is_temporary_directory(path: str) -> bool:
+    try:
+        tmpdir = tempfile.gettempdir()
+        return os.path.commonpath([path, tmpdir]) == tmpdir and os.path.exists(path) and os.path.isdir(path)
+    except Exception:
+        return False

From 11b4fa2cd40bfcf1cb3a7a751ae74cbe13e8f7a7 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 15 May 2024 10:02:31 -0400
Subject: [PATCH 38/46] version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 0cd50ccff..f6846b488 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b31"  # TODO: To become 8.8.5
+version = "8.8.4.1b32"  # 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"

From e61027b8d6d32d5cdade1957d217ea2eb2b0e2ff Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Fri, 17 May 2024 06:48:01 -0400
Subject: [PATCH 39/46] corrected type hint in file_utils.search_for_file

---
 dcicutils/file_utils.py | 6 +++---
 pyproject.toml          | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/dcicutils/file_utils.py b/dcicutils/file_utils.py
index 0ebc8e4cd..405ffb454 100644
--- a/dcicutils/file_utils.py
+++ b/dcicutils/file_utils.py
@@ -14,7 +14,7 @@
 
 
 def search_for_file(file: str,
-                    location: Union[str, Optional[List[str]]] = None,
+                    location: Union[str, pathlib.PosixPath, Optional[List[Union[str, pathlib.PosixPath]]]] = None,
                     recursive: bool = False,
                     single: bool = False,
                     order: bool = True) -> Union[List[str], Optional[str]]:
@@ -35,7 +35,7 @@ def order_by(path: str):
         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 str(file) if single is True else [str(file)]
         return None if single is True else []
     files_found = []
     if not location:
@@ -53,7 +53,7 @@ def order_by(path: str):
         if not (directory := directory.strip()):
             continue
         if os.path.isfile(directory := os.path.abspath(os.path.normpath(directory))):
-            # Allow a file; assume its parent directory was intended.
+            # Actually, allow a file rather then a directory; assume its parent directory was intended.
             if not (directory := os.path.dirname(directory)):
                 continue
         if directory not in location_pruned:
diff --git a/pyproject.toml b/pyproject.toml
index f6846b488..75d334bfe 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b32"  # TODO: To become 8.8.5
+version = "8.8.4.1b33"  # 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"

From b54476fbaa7d9d02df1356cc96ff602259602ea9 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Sun, 19 May 2024 18:09:59 -0400
Subject: [PATCH 40/46] minor tidy up of format_size output; remove extraneous
 trailing zeros.

---
 dcicutils/misc_utils.py | 9 ++++++++-
 pyproject.toml          | 2 +-
 2 files changed, 9 insertions(+), 2 deletions(-)

diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 56e5a0b34..ddac5f42d 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -2606,7 +2606,11 @@ def format_size(nbytes: Union[int, float], precision: int = 2, nospace: bool = F
         nbytes = int(nbytes)
         return f"{nbytes} byte{'s' if nbytes != 1 else ''}"
     unit = (UNITS_TERSE if terse else UNITS)[index]
-    return f"{nbytes:.{precision}f}{'' if nospace else ' '}{unit}"
+    size = f"{nbytes:.{precision}f}"
+    if size.endswith(f".{'0' * precision}"):
+        # Tidy up extraneous zeros.
+        size = size[:-(precision - 1)]
+    return f"{size}{'' if nospace else ' '}{unit}"
 
 
 def format_duration(seconds: Union[int, float]) -> str:
@@ -2731,3 +2735,6 @@ def create_short_uuid(length: Optional[int] = None, upper: bool = False):
     if upper is True:
         value = value.upper()
     return value
+
+
+print(format_size(1024 * 1024))
diff --git a/pyproject.toml b/pyproject.toml
index 75d334bfe..c23c1467e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b33"  # TODO: To become 8.8.5
+version = "8.8.4.1b34"  # 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"

From 10d8a55d332954eef1637e7109ac7b125e3e83c1 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Sun, 19 May 2024 22:08:55 -0400
Subject: [PATCH 41/46] removed cruft in misc_utils

---
 dcicutils/misc_utils.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index ddac5f42d..060ca95ec 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -2735,6 +2735,3 @@ def create_short_uuid(length: Optional[int] = None, upper: bool = False):
     if upper is True:
         value = value.upper()
     return value
-
-
-print(format_size(1024 * 1024))

From c2fefc4c3e23c093fc1a921b0e14911bbc4fd44b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Sun, 19 May 2024 22:09:04 -0400
Subject: [PATCH 42/46] versino

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index c23c1467e..f0bef193a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b34"  # TODO: To become 8.8.5
+version = "8.8.4.1b35"  # 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"

From dbea70126d369b3aadf2baba2f897f3904305315 Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 22 May 2024 15:46:22 -0400
Subject: [PATCH 43/46] Added remove_empty_objects_from_lists support in
 structured_data.

---
 CHANGELOG.rst                |  3 +++
 dcicutils/misc_utils.py      | 18 +++++++++++++---
 dcicutils/structured_data.py | 27 ++++++++++++++++++++----
 pyproject.toml               |  2 +-
 test/test_structured_data.py | 40 ++++++++++++++++++++++++++++++++----
 5 files changed, 78 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 507f919d1..eb4ce6e0d 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -14,6 +14,9 @@ Change Log
   for running Foursight checks locally (with local ssh tunnel to ES proxy);
   came up in foursight/checks/audit_checks (2024-04-23).
 * Allow Python 3.12 (pyproject.toml).
+* Added remove_empty_objects_from_lists options to structured_data.StructuredDataSet, defaulting
+  to True, which deletes empty objects from lists; however, only from the *end* of a list; if
+  this flag is True and there are non-empty objects following empty objects then we flag an error.
 * Few general things initially related to and factored out of rclone support in smaht-submitr:
   - Added extract_file_from_zip to zip_utils.
   - Added http_utils with download function.
diff --git a/dcicutils/misc_utils.py b/dcicutils/misc_utils.py
index 060ca95ec..0d719c421 100644
--- a/dcicutils/misc_utils.py
+++ b/dcicutils/misc_utils.py
@@ -1155,7 +1155,8 @@ def remove_suffix(suffix: str, text: str, required: bool = False):
 
 def remove_empty_properties(data: Optional[Union[list, dict]],
                             isempty: Optional[Callable] = None,
-                            isempty_array_element: Optional[Callable] = None) -> None:
+                            isempty_array_element: Optional[Callable] = None,
+                            raise_exception_on_nonempty_array_element_after_empty: bool = False) -> None:
     def _isempty(value: Any) -> bool:  # noqa
         return isempty(value) if callable(isempty) else value in [None, "", {}, []]
     if isinstance(data, dict):
@@ -1163,11 +1164,22 @@ def _isempty(value: Any) -> bool:  # noqa
             if _isempty(value := data[key]):
                 del data[key]
             else:
-                remove_empty_properties(value, isempty=isempty, isempty_array_element=isempty_array_element)
+                remove_empty_properties(value, isempty=isempty, isempty_array_element=isempty_array_element,
+                                        raise_exception_on_nonempty_array_element_after_empty=  # noqa
+                                        raise_exception_on_nonempty_array_element_after_empty)
     elif isinstance(data, list):
         for item in data:
-            remove_empty_properties(item, isempty=isempty, isempty_array_element=isempty_array_element)
+            remove_empty_properties(item, isempty=isempty, isempty_array_element=isempty_array_element,
+                                    raise_exception_on_nonempty_array_element_after_empty=  # noqa
+                                    raise_exception_on_nonempty_array_element_after_empty)
         if callable(isempty_array_element):
+            if raise_exception_on_nonempty_array_element_after_empty is True:
+                empty_element_seen = False
+                for item in data:
+                    if not empty_element_seen and isempty_array_element(item):
+                        empty_element_seen = True
+                    elif empty_element_seen and not isempty_array_element(item):
+                        raise Exception("Non-empty element found after empty element.")
             data[:] = [item for item in data if not isempty_array_element(item)]
 
 
diff --git a/dcicutils/structured_data.py b/dcicutils/structured_data.py
index 36ee036f8..e80caf637 100644
--- a/dcicutils/structured_data.py
+++ b/dcicutils/structured_data.py
@@ -53,6 +53,7 @@ class StructuredDataSet:
     def __init__(self, file: Optional[str] = None, portal: Optional[Union[VirtualApp, TestApp, Portal]] = None,
                  schemas: Optional[List[dict]] = None, autoadd: Optional[dict] = None,
                  order: Optional[List[str]] = None, prune: bool = True,
+                 remove_empty_objects_from_lists: bool = True,
                  ref_lookup_strategy: Optional[Callable] = None,
                  ref_lookup_nocache: bool = False,
                  norefs: bool = False,
@@ -65,7 +66,8 @@ def __init__(self, file: Optional[str] = None, portal: Optional[Union[VirtualApp
                               ref_lookup_nocache=ref_lookup_nocache) if portal else None
         self._ref_lookup_strategy = ref_lookup_strategy
         self._order = order
-        self._prune = prune
+        self._prune = prune is True
+        self._remove_empty_objects_from_lists = remove_empty_objects_from_lists is True
         self._warnings = {}
         self._errors = {}
         self._resolved_refs = set()
@@ -93,12 +95,14 @@ def portal(self) -> Optional[Portal]:
     def load(file: str, portal: Optional[Union[VirtualApp, TestApp, Portal]] = None,
              schemas: Optional[List[dict]] = None, autoadd: Optional[dict] = None,
              order: Optional[List[str]] = None, prune: bool = True,
+             remove_empty_objects_from_lists: bool = True,
              ref_lookup_strategy: Optional[Callable] = None,
              ref_lookup_nocache: bool = False,
              norefs: bool = False,
              progress: Optional[Callable] = None,
              debug_sleep: Optional[str] = None) -> StructuredDataSet:
         return StructuredDataSet(file=file, portal=portal, schemas=schemas, autoadd=autoadd, order=order, prune=prune,
+                                 remove_empty_objects_from_lists=remove_empty_objects_from_lists,
                                  ref_lookup_strategy=ref_lookup_strategy, ref_lookup_nocache=ref_lookup_nocache,
                                  norefs=norefs, progress=progress, debug_sleep=debug_sleep)
 
@@ -368,7 +372,11 @@ def _load_reader(self, reader: RowReader, type_name: str) -> None:
                 structured_row_template.set_value(structured_row, column_name, value, reader.file, reader.row_number)
                 if self._autoadd_properties:
                     self._add_properties(structured_row, self._autoadd_properties, schema)
-            self._add(type_name, structured_row)
+            if (prune_error := self._prune_structured_row(structured_row)) is not None:
+                self._note_error({"src": create_dict(type=schema_name, row=reader.row_number),
+                                  "error": prune_error}, "validation")
+            else:
+                self._add(type_name, structured_row)
             if self._progress:
                 self._progress({
                     PROGRESS.LOAD_ITEM: self._nrows,
@@ -385,9 +393,20 @@ def _load_reader(self, reader: RowReader, type_name: str) -> None:
             self._note_error(schema._unresolved_refs, "ref")
             self._resolved_refs.update(schema._resolved_refs)
 
-    def _add(self, type_name: str, data: Union[dict, List[dict]]) -> None:
-        if self._prune:
+    def _prune_structured_row(self, data: dict) -> Optional[str]:
+        if not self._prune:
+            return None
+        if not self._remove_empty_objects_from_lists:
             remove_empty_properties(data)
+            return None
+        try:
+            remove_empty_properties(data, isempty_array_element=lambda element: element == {},
+                                    raise_exception_on_nonempty_array_element_after_empty=True)
+        except Exception as e:
+            return str(e)
+        return None
+
+    def _add(self, type_name: str, data: Union[dict, List[dict]]) -> None:
         if type_name in self._data:
             self._data[type_name].extend([data] if isinstance(data, dict) else data)
         else:
diff --git a/pyproject.toml b/pyproject.toml
index f0bef193a..421985fb9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b35"  # TODO: To become 8.8.5
+version = "8.8.4.1b36"  # 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"
diff --git a/test/test_structured_data.py b/test/test_structured_data.py
index a1b713762..453ce32bc 100644
--- a/test/test_structured_data.py
+++ b/test/test_structured_data.py
@@ -943,9 +943,37 @@ def _pytest_kwargs(kwargs: List[dict]) -> List[dict]:
                 }
             }
         ],
-        # "expected": {"Test": [{"arrayofobject": [{"name": "anastasiia", "id": 1234}]}]},
         "expected": {"Test": [{"arrayofobject": [{}, {}, {"name": "olha", "id": 5678},
-                                                 {}, {"name": "anastasiia", "id": 1234}]}]}
+                                                 {}, {"name": "anastasiia", "id": 1234}]}]},
+        "remove_empty_objects_from_lists": False
+    },
+    # ----------------------------------------------------------------------------------------------
+    {
+        "rows": [
+            "arrayofobject#0.name,arrayofobject#0.id,arrayofobject#1.name,arrayofobject#1.id,"
+            "arrayofobject#2.name,arrayofobject#2.id",
+            "anastasiia,1234,olha,5678,,"
+        ],
+        "as_file_name": "test.csv",
+        "schemas": [
+            {
+                "title": "Test",
+                "properties": {
+                    "arrayofobject": {
+                        "type": "array",
+                        "items": {
+                            "type": "object",
+                            "properties": {
+                                "name": {"type": "string"},
+                                "id": {"type": "integer"}
+                            }
+                        }
+                    }
+                }
+            }
+        ],
+        "expected": {"Test": [{"arrayofobject": [{"name": "anastasiia", "id": 1234},
+                                                 {"name": "olha", "id": 5678}]}]}
     },
     # ----------------------------------------------------------------------------------------------
     {
@@ -1332,6 +1360,7 @@ def _test_parse_structured_data(testapp,
                                 schemas: Optional[List[dict]] = None,
                                 autoadd: Optional[dict] = None,
                                 prune: bool = True,
+                                remove_empty_objects_from_lists: bool = True,
                                 ignore: bool = False,
                                 debug: bool = False) -> None:
 
@@ -1360,12 +1389,13 @@ def _test_parse_structured_data(testapp,
     def assert_parse_structured_data():
 
         def call_parse_structured_data(file: str):
-            nonlocal portal, novalidate, autoadd, prune, debug
+            nonlocal portal, novalidate, autoadd, prune, remove_empty_objects_from_lists, debug
             if debug:
                 # import pdb ; pdb.set_trace()
                 pass
             return parse_structured_data(file=file, portal=portal, novalidate=novalidate,
-                                         autoadd=autoadd, prune=True if prune is not False else False)
+                                         autoadd=autoadd, prune=True if prune is not False else False,
+                                         remove_empty_objects_from_lists=remove_empty_objects_from_lists)
 
         nonlocal file, expected, expected_errors, schemas, noschemas, debug
         portal = Portal(testapp, schemas=schemas) if not noschemas else None  # But see mocked_schemas.
@@ -1511,6 +1541,7 @@ def is_accession(value: str) -> bool:
 # Same as in smaht-portal/../ingestion_processors.py
 def parse_structured_data(file: str, portal: Optional[Union[VirtualApp, TestApp, Portal]], novalidate: bool = False,
                           autoadd: Optional[dict] = None, prune: bool = True,
+                          remove_empty_objects_from_lists: bool = True,
                           ref_nocache: bool = False) -> StructuredDataSet:
 
     def ref_lookup_strategy(portal: Portal, type_name: str, schema: dict, value: str) -> Tuple[int, Optional[str]]:
@@ -1528,6 +1559,7 @@ def ref_lookup_strategy(portal: Portal, type_name: str, schema: dict, value: str
 
     structured_data = StructuredDataSet.load(file=file, portal=portal,
                                              autoadd=autoadd, order=ITEM_INDEX_ORDER, prune=prune,
+                                             remove_empty_objects_from_lists=remove_empty_objects_from_lists,
                                              ref_lookup_strategy=ref_lookup_strategy,
                                              ref_lookup_nocache=ref_nocache)
     if not novalidate:

From 590efcf8e2803a27fe66120e51ac6acf470b5bcd Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Wed, 22 May 2024 22:12:38 -0400
Subject: [PATCH 44/46] better handle json files (unusual case) in
 structured_data

---
 dcicutils/structured_data.py | 13 ++++++++++++-
 pyproject.toml               |  2 +-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/dcicutils/structured_data.py b/dcicutils/structured_data.py
index e80caf637..6d489ea17 100644
--- a/dcicutils/structured_data.py
+++ b/dcicutils/structured_data.py
@@ -350,7 +350,18 @@ def get_counts() -> Tuple[int, int]:
 
     def _load_json_file(self, file: str) -> None:
         with open(file) as f:
-            self._add(Schema.type_name(file), json.load(f))
+            file_json = json.load(f)
+            schema_inferred_from_file_name = Schema.type_name(file)
+            if self._portal.get_schema(schema_inferred_from_file_name) is not None:
+                # If the JSON file name looks like a schema name then assume it
+                # contains an object or an array of object of that schema type.
+                self._add(Schema.type_name(file), file_json)
+            elif isinstance(file_json, dict):
+                # Otherwise if the JSON file name does not look like a schema name then
+                # assume it a dictionary where each property is the name of a schema, and
+                # which (each property) contains a list of object of that schema type.
+                for schema_name in file_json:
+                    self._add(schema_name, file_json[schema_name])
 
     def _load_reader(self, reader: RowReader, type_name: str) -> None:
         schema = None
diff --git a/pyproject.toml b/pyproject.toml
index 421985fb9..97f5f588e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b36"  # TODO: To become 8.8.5
+version = "8.8.4.1b37"  # 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"

From a17ebc50e9d192584a0d67c2ca575cc23d83234b Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 23 May 2024 06:44:15 -0400
Subject: [PATCH 45/46] minor updates to
 dcicutils/scripts/view_portal_object.py

---
 CHANGELOG.rst                           |  1 +
 dcicutils/scripts/view_portal_object.py | 92 +++++++++++++++++++++++--
 pyproject.toml                          |  2 +-
 3 files changed, 89 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index eb4ce6e0d..5b4512fe2 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -27,6 +27,7 @@ Change Log
   - Added deterministic ordering to paths returned by search_for_file in file_utils.
   - Added create_temporary_file_name and remove_temporary_file tmpfile_utils.
   - Minor fix to misc_utils.create_dict (do not create property only if its value is None).
+  - Minor updates to utility dcicutils.scripts.view_portal_object.
 
 
 8.8.4
diff --git a/dcicutils/scripts/view_portal_object.py b/dcicutils/scripts/view_portal_object.py
index 55b0430b1..28097bf7b 100644
--- a/dcicutils/scripts/view_portal_object.py
+++ b/dcicutils/scripts/view_portal_object.py
@@ -57,6 +57,7 @@
 
 import argparse
 from functools import lru_cache
+import io
 import json
 import pyperclip
 import os
@@ -97,11 +98,18 @@ def main():
                         help="Include all properties for schema usage.")
     parser.add_argument("--raw", action="store_true", required=False, default=False, help="Raw output.")
     parser.add_argument("--tree", action="store_true", required=False, default=False, help="Tree output for schemas.")
+    parser.add_argument("--post", type=str, required=False, default=None,
+                        help="POST data of the main arg type with data from file specified with this option.")
+    parser.add_argument("--patch", type=str, required=False, default=None,
+                        help="PATCH data of the main arg type with data from file specified with this option.")
     parser.add_argument("--database", action="store_true", required=False, default=False,
                         help="Read from database output.")
+    parser.add_argument("--bool", action="store_true", required=False,
+                        default=False, help="Only return whether found or not.")
     parser.add_argument("--yaml", action="store_true", required=False, default=False, help="YAML output.")
     parser.add_argument("--copy", "-c", action="store_true", required=False, default=False,
                         help="Copy object data to clipboard.")
+    parser.add_argument("--indent", required=False, default=False, help="Indent output.", type=int)
     parser.add_argument("--details", action="store_true", required=False, default=False, help="Detailed output.")
     parser.add_argument("--more-details", action="store_true", required=False, default=False,
                         help="More detailed output.")
@@ -151,6 +159,18 @@ def main():
         args.schema = True
 
     if args.schema:
+        if args.post:
+            if post_data := _read_json_from_file(args.post):
+                if args.verbose:
+                    _print(f"POSTing data from file ({args.post}) as type: {args.uuid}")
+                if isinstance(post_data, dict):
+                    post_data = [post_data]
+                elif not isinstance(post_data, list):
+                    _print(f"POST data neither list nor dictionary: {args.post}")
+                for item in post_data:
+                    portal.post_metadata(args.uuid, item)
+                if args.verbose:
+                    _print(f"Done POSTing data from file ({args.post}) as type: {args.uuid}")
         schema, schema_name = _get_schema(portal, args.uuid)
         if schema:
             if args.copy:
@@ -166,14 +186,50 @@ def main():
             _print_schema(schema, details=args.details, more_details=args.details,
                           all=args.all, raw=args.raw, raw_yaml=args.yaml)
             return
-
-    data = _get_portal_object(portal=portal, uuid=args.uuid, raw=args.raw, database=args.database, verbose=args.verbose)
+    elif args.patch:
+        if patch_data := _read_json_from_file(args.patch):
+            if args.verbose:
+                _print(f"PATCHing data from file ({args.patch}) for object: {args.uuid}")
+            if isinstance(patch_data, dict):
+                patch_data = [patch_data]
+            elif not isinstance(patch_data, list):
+                _print(f"PATCH data neither list nor dictionary: {args.patch}")
+            for item in patch_data:
+                portal.patch_metadata(args.uuid, item)
+            if args.verbose:
+                _print(f"Done PATCHing data from file ({args.patch}) as type: {args.uuid}")
+            return
+        else:
+            _print(f"No PATCH data found in file: {args.patch}")
+            exit(1)
+
+    data = _get_portal_object(portal=portal, uuid=args.uuid, raw=args.raw,
+                              database=args.database, check=args.bool, verbose=args.verbose)
+    if args.bool:
+        if data:
+            _print(f"{args.uuid}: found")
+            exit(0)
+        else:
+            _print(f"{args.uuid}: not found")
+            exit(1)
     if args.copy:
         pyperclip.copy(json.dumps(data, indent=4))
     if args.yaml:
         _print(yaml.dump(data))
     else:
-        _print(json.dumps(data, default=str, indent=4))
+        if args.indent > 0:
+            _print(_format_json_with_indent(data, indent=args.indent))
+        else:
+            _print(json.dumps(data, default=str, indent=4))
+
+
+def _format_json_with_indent(value: dict, indent: int = 0) -> Optional[str]:
+    if isinstance(value, dict):
+        result = json.dumps(value, indent=4)
+        if indent > 0:
+            result = f"{indent * ' '}{result}"
+            result = result.replace("\n", f"\n{indent * ' '}")
+        return result
 
 
 def _create_portal(ini: str, env: Optional[str] = None,
@@ -198,7 +254,8 @@ def _create_portal(ini: str, env: Optional[str] = None,
 
 
 def _get_portal_object(portal: Portal, uuid: str,
-                       raw: bool = False, database: bool = False, verbose: bool = False) -> dict:
+                       raw: bool = False, database: bool = False,
+                       check: bool = False, verbose: bool = False) -> dict:
     response = None
     try:
         if not uuid.startswith("/"):
@@ -212,13 +269,18 @@ def _get_portal_object(portal: Portal, uuid: str,
             _exit()
         _exit(f"Exception getting Portal object from {portal.server}: {uuid}\n{get_error_message(e)}")
     if not response:
+        if check:
+            return None
         _exit(f"Null response getting Portal object from {portal.server}: {uuid}")
     if response.status_code not in [200, 307]:
         # TODO: Understand why the /me endpoint returns HTTP status code 307, which is only why we mention it above.
         _exit(f"Invalid status code ({response.status_code}) getting Portal object from {portal.server}: {uuid}")
     if not response.json:
         _exit(f"Invalid JSON getting Portal object: {uuid}")
-    return response.json()
+    response = response.json()
+    if raw:
+        response.pop("schema_version", None)
+    return response
 
 
 @lru_cache(maxsize=1)
@@ -257,6 +319,7 @@ def _print_schema_info(schema: dict, level: int = 0,
                        required: Optional[List[str]] = None) -> None:
     if not schema or not isinstance(schema, dict):
         return
+    identifying_properties = schema.get("identifyingProperties")
     if level == 0:
         if required_properties := schema.get("required"):
             _print("- required properties:")
@@ -383,6 +446,8 @@ def _print_schema_info(schema: dict, level: int = 0,
                         suffix += f" | enum"
                     if property_required:
                         suffix += f" | required"
+                    if property_name in (identifying_properties or []):
+                        suffix += f" | identifying"
                     if property.get("uniqueKey"):
                         suffix += f" | unique"
                     if pattern := property.get("pattern"):
@@ -529,6 +594,23 @@ def tree_generator(name: str, prefix: str = ""):
         print(line)
 
 
+def _read_json_from_file(file: str) -> Optional[dict]:
+    if not os.path.exists(file):
+        _print(f"Cannot find file: {file}")
+        exit(1)
+    try:
+        with io.open(file, "r") as f:
+            try:
+                return json.load(f)
+            except Exception:
+                _print(f"Cannot parse JSON in file: {file}")
+                exit(1)
+    except Exception as e:
+        print(e)
+        _print(f"Cannot open file: {file}")
+        exit(1)
+
+
 def _print(*args, **kwargs):
     with uncaptured_output():
         PRINT(*args, **kwargs)
diff --git a/pyproject.toml b/pyproject.toml
index 97f5f588e..328db02c3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b37"  # TODO: To become 8.8.5
+version = "8.8.4.1b38"  # 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"

From 41f8f751e7ce1f58cba182021bd4e7e5491f70cd Mon Sep 17 00:00:00 2001
From: David Michaels <david_michaels@hms.harvard.edu>
Date: Thu, 23 May 2024 07:34:04 -0400
Subject: [PATCH 46/46] version

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 328db02c3..11db8d2a3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.8.4.1b38"  # TODO: To become 8.8.5
+version = "8.8.4.1b39"  # 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"