dcicutils 8.7.2.1b1__tar.gz → 8.7.2.1b3__tar.gz

{dcicutils-8.7.2.1b1 → dcicutils-8.7.2.1b3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.7.2.1b1
+Version: 8.7.2.1b3
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT
@@ -36,6 +36,7 @@ Requires-Dist: jsonschema (>=4.19.0,<5.0.0)
 Requires-Dist: openpyxl (>=3.1.2,<4.0.0)
 Requires-Dist: opensearch-py (>=2.0.1,<3.0.0)
 Requires-Dist: pyOpenSSL (>=23.1.1,<24.0.0)
+Requires-Dist: pyperclip (>=1.8.2,<2.0.0)
 Requires-Dist: pyramid (==1.10.4)
 Requires-Dist: pytz (>=2020.4)
 Requires-Dist: redis (>=4.5.1,<5.0.0)

dcicutils-8.7.2.1b3/dcicutils/captured_output.py

@@ -0,0 +1,70 @@
+from collections import namedtuple
+from contextlib import contextmanager
+import io
+import sys
+from typing import Optional
+
+_real_stdout = sys.stdout
+_real_stderr = sys.stderr
+
+
+@contextmanager
+def captured_output(capture: bool = True):
+    """
+    Context manager to capture any/all output to stdout or stderr, and not actually output it to stdout
+    or stderr. Yields and object with a get_captured_output() method to get the output captured thus far,
+    and another uncaptured_print() method to actually print the given output to stdout, even though output
+    to stdout is being captured. Can be useful, for example, in creating command-line scripts which invoke
+    code which outputs a lot of info, warning, error, etc to stdout or stderr, and we want to suprress that
+    output; but with the yielded uncaptured_print() method output specific to the script can actually be
+    output (to stdout); and/or can also optionally output any/all captured output, e.g. for debugging or
+    troubleshooting purposes. Disable this capture, without having to restructure your code WRT the usage
+    of the with-clause with this context manager, pass False as an argument to this context manager.
+    """
+
+    original_stdout = _real_stdout
+    original_stderr = _real_stderr
+    captured_output = io.StringIO()
+
+    def set_original_output() -> None:
+        sys.stdout = original_stdout
+        sys.stderr = original_stderr
+
+    def set_captured_output() -> None:
+        if capture:
+            sys.stdout = captured_output
+            sys.stderr = captured_output
+
+    def uncaptured_print(*args, **kwargs) -> None:
+        set_original_output()
+        print(*args, **kwargs)
+        set_captured_output()
+
+    def uncaptured_input(message: str) -> str:
+        set_original_output()
+        value = input(message)
+        set_captured_output()
+        return value
+
+    def get_captured_output() -> Optional[str]:
+        return captured_output.getvalue() if capture else None
+
+    try:
+        set_captured_output()
+        Result = namedtuple("Result", ["get_captured_output", "uncaptured_print", "uncaptured_input"])
+        yield Result(get_captured_output, uncaptured_print, uncaptured_input)
+    finally:
+        set_original_output()
+
+
+@contextmanager
+def uncaptured_output():
+    original_stdout = sys.stdout
+    original_stderr = sys.stderr
+    sys.stdout = _real_stdout
+    sys.stderr = _real_stderr
+    try:
+        yield
+    finally:
+        sys.stdout = original_stdout
+        sys.stderr = original_stderr

{dcicutils-8.7.2.1b1 → dcicutils-8.7.2.1b3}/dcicutils/data_readers.py

@@ -152,9 +152,10 @@ class ExcelSheetReader(RowReader):
 
 class Excel:
 
-    def __init__(self, file: str, reader_class: Optional[Type] = None) -> None:
+    def __init__(self, file: str, reader_class: Optional[Type] = None, include_hidden_sheets: bool = False) -> None:
         self._file = file
         self._workbook = None
+        self._include_hidden_sheets = include_hidden_sheets
         self.sheet_names = None
         if isinstance(reader_class, Type) and issubclass(reader_class, ExcelSheetReader):
             self._reader_class = reader_class
@@ -169,7 +170,7 @@ class Excel:
         if self._workbook is None:
             self._workbook = openpyxl.load_workbook(self._file, data_only=True)
             self.sheet_names = [sheet_name for sheet_name in self._workbook.sheetnames
-                                if self._workbook[sheet_name].sheet_state != "hidden"]
+                                if self._include_hidden_sheets or (self._workbook[sheet_name].sheet_state != "hidden")]
 
     def __del__(self) -> None:
         if (workbook := self._workbook) is not None:

{dcicutils-8.7.2.1b1 → dcicutils-8.7.2.1b3}/dcicutils/datetime_utils.py

@@ -65,7 +65,7 @@ def normalize_datetime_string(value: str) -> Optional[str]:
     or if ill-formated then returns None. The given string is assumed to be in the format "YYYY-MM-DD hh:mm:ss"
     and with an optional timezone suffix in format "+hh:mm" or "+hh". Also allowed is just a date of the
     format "YYYY-MM-DD" in which case a time of "00:00:00" is assumed. If no timezone is specified then
-    the local timezone is assumed.  The returned format looks like this: "2024-02-08T10:37:51-05:00"
+    the local timezone is assumed. The returned format looks like this: "2024-02-08T10:37:51-05:00"
     """
     dt = parse_datetime_string(value)
     return dt.isoformat() if dt else None

dcicutils-8.7.2.1b3/dcicutils/scripts/view_portal_object.py

@@ -0,0 +1,155 @@
+# ------------------------------------------------------------------------------------------------------
+# Command-line utility to retrieve and print the given object (UUID) from a SMaHT/CGAP/Fourfront Portal.
+# ------------------------------------------------------------------------------------------------------
+# Example command:
+#  view-portal-object 4483b19d-62e7-4e7f-a211-0395343a35df --yaml
+#
+# Example output:
+#  '@context': /terms/
+#  '@id': /access-keys/3968e38e-c11f-472e-8531-8650e2e296d4/
+#  '@type':
+#  - AccessKey
+#  - Item
+#  access_key_id: NSVCZ75O
+#  date_created: '2023-09-06T13:11:59.704005+00:00'
+#  description: Manually generated local access-key for testing.
+#  display_title: AccessKey from 2023-09-06
+#  expiration_date: '2023-12-05T13:11:59.714106'
+#  last_modified:
+#    date_modified: '2023-09-06T13:11:59.711367+00:00'
+#    modified_by:
+#      '@id': /users/3202fd57-44d2-44fb-a131-afb1e43d8ae5/
+#      '@type':
+#      - User
+#      - Item
+#      status: current
+#      uuid: 3202fd57-44d2-44fb-a131-afb1e43d8ae5
+#  principals_allowed:
+#    edit:
+#    - group.admin
+#    - userid.74fef71a-dfc1-4aa4-acc0-cedcb7ac1d68
+#    view:
+#    - group.admin
+#    - group.read-only-admin
+#    - userid.74fef71a-dfc1-4aa4-acc0-cedcb7ac1d68
+#  schema_version: '1'
+#  status: current
+#  user:
+#    '@id': /users/74fef71a-dfc1-4aa4-acc0-cedcb7ac1d68/
+#    '@type':
+#    - User
+#    - Item
+#    display_title: David Michaels
+#    principals_allowed:
+#      edit:
+#      - group.admin
+#      view:
+#      - group.admin
+#      - group.read-only-admin
+#    status: current
+#    uuid: 74fef71a-dfc1-4aa4-acc0-cedcb7ac1d68
+#  uuid: 3968e38e-c11f-472e-8531-8650e2e296d4
+#
+# Note that instead of a uuid you can also actually use a path, for example:
+#   view-local-object /file-formats/vcf_gz_tbi
+#
+# --------------------------------------------------------------------------------------------------
+
+import argparse
+import json
+import pyperclip
+import sys
+from typing import Optional
+import yaml
+from dcicutils.misc_utils import get_error_message
+from dcicutils.portal_utils import Portal
+from dcicutils.captured_output import captured_output, uncaptured_output
+
+
+def main():
+
+    parser = argparse.ArgumentParser(description="View Portal object.")
+    parser.add_argument("uuid", type=str,
+                        help=f"The uuid (or path) of the object to fetch and view. ")
+    parser.add_argument("--ini", type=str, required=False, default=None,
+                        help=f"Name of the application .ini file.")
+    parser.add_argument("--env", "-e", type=str, required=False, default=None,
+                        help=f"Environment name (key from ~/.smaht-keys.json).")
+    parser.add_argument("--server", "-s", type=str, required=False, default=None,
+                        help=f"Environment server name (server from key in ~/.smaht-keys.json).")
+    parser.add_argument("--app", type=str, required=False, default=None,
+                        help=f"Application name (one of: smaht, cgap, fourfront).")
+    parser.add_argument("--raw", action="store_true", required=False, default=False, help="Raw output.")
+    parser.add_argument("--database", action="store_true", required=False, default=False,
+                        help="Read from database output.")
+    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("--verbose", action="store_true", required=False, default=False, help="Verbose output.")
+    parser.add_argument("--debug", action="store_true", required=False, default=False, help="Debugging output.")
+    args = parser.parse_args()
+
+    portal = _create_portal(ini=args.ini, env=args.env, server=args.server, app=args.app, debug=args.debug)
+    data = _get_portal_object(portal=portal, uuid=args.uuid, raw=args.raw, database=args.database, verbose=args.verbose)
+
+    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))
+
+
+def _create_portal(ini: str, env: Optional[str] = None,
+                   server: Optional[str] = None, app: Optional[str] = None, debug: bool = False) -> Portal:
+    with captured_output(not debug):
+        return Portal(env, server=server, app=app) if env or app else Portal(ini)
+
+
+def _get_portal_object(portal: Portal, uuid: str,
+                       raw: bool = False, database: bool = False, verbose: bool = False) -> dict:
+    if verbose:
+        _print(f"Getting object ({uuid}) from portal ... ", end="")
+    response = None
+    try:
+        if not uuid.startswith("/"):
+            path = f"/{uuid}"
+        else:
+            path = uuid
+        response = portal.get(path, raw=raw, database=database)
+    except Exception as e:
+        if "404" in str(e) and "not found" in str(e).lower():
+            if verbose:
+                _print("Not found!")
+            else:
+                _print(f"Object ({uuid}) not found!")
+            _exit_without_action()
+        _exit_without_action(f"Exception getting object ({uuid}) -> {get_error_message(e)}", newline=verbose)
+    if not response:
+        _exit_without_action(f"Null response getting object {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_without_action(f"Invalid status code ({response.status_code}) getting object: {uuid}")
+    if not response.json:
+        _exit_without_action(f"Invalid JSON getting object {uuid}).")
+    if verbose:
+        _print("OK")
+    return response.json()
+
+
+def _print(*args, **kwargs):
+    with uncaptured_output():
+        print(*args, **kwargs)
+    sys.stdout.flush()
+
+
+def _exit_without_action(message: Optional[str] = None, newline: bool = True) -> None:
+    if message:
+        if newline:
+            _print()
+        _print(f"ERROR: {message}")
+    exit(1)
+
+
+if __name__ == "__main__":
+    main()

{dcicutils-8.7.2.1b1 → dcicutils-8.7.2.1b3}/dcicutils/structured_data.py

@@ -717,7 +717,7 @@ class Portal(PortalBase):
             for item in items:
                 if (ivalue := next((item[iproperty] for iproperty in iproperties if iproperty in item), None)):
                     if isinstance(ivalue, list) and value in ivalue or ivalue == value:
-                        return True, ivalue if is_uuid(ivalue) else None
+                        return True, (ivalue if isinstance(ivalue, str) and is_uuid(ivalue) else None)
         if (value := self.get_metadata(f"/{type_name}/{value}")) is None:
             return False, None
         return True, value.get("uuid")

{dcicutils-8.7.2.1b1 → dcicutils-8.7.2.1b3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.7.2.1b1"  # TODO: To become 8.8.0
+version = "8.7.2.1b3"  # TODO: To become 8.8.0
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -56,6 +56,7 @@ PyJWT = "^2.6.0"
 pyramid = "1.10.4"
 pytz = ">=2020.4"
 redis = "^4.5.1"
+pyperclip = "^1.8.2"
 PyYAML = "^6.0.1"
 requests = "^2.21.0"
 rfc3986 = "^1.4.0"
@@ -88,6 +89,7 @@ pytest-runner = ">=5.1"
 publish-to-pypi = "dcicutils.scripts.publish_to_pypi:main"
 show-contributors = "dcicutils.contribution_scripts:show_contributors_main"
 run-license-checker = "dcicutils.scripts.run_license_checker:main"
+view-portal-object = "dcicutils.scripts.view_portal_object:main"
 
 
 [tool.pytest.ini_options]