dcicutils 8.11.0__py3-none-any.whl → 8.11.0.1b1__py3-none-any.whl

dcicutils/command_utils.py

@@ -7,6 +7,7 @@ import os
 import re
 import requests
 import subprocess
+import sys
 
 from typing import Callable, Optional
 from .exceptions import InvalidParameterError
@@ -372,7 +373,7 @@ def script_catch_errors():
         raise ScriptFailure(' '.join(message))
     try:
         yield fail
-        exit(0)
+        sys.exit(0)
     except (Exception, ScriptFailure) as e:
         if DEBUG_SCRIPT:
             # If debugging, let the error propagate, do not trap it.
@@ -384,7 +385,7 @@ def script_catch_errors():
             else:
                 message = str(e)  # Note: We ignore the type, which isn't intended to be shown.
                 PRINT(message)
-            exit(1)
+            sys.exit(1)
 
 
 class Question:

dcicutils/deployment_utils.py

@@ -396,9 +396,9 @@ class EBDeployer:
             packaging_was_successful = cls.build_application_version(args.repo, args.version_name, branch=args.branch)
             if packaging_was_successful:  # XXX: how to best detect?
                 time.sleep(5)  # give EB a second to catch up (it needs it)
-                exit(cls.deploy_new_version(args.env, args.repo, args.version_name))
+                sys.exit(cls.deploy_new_version(args.env, args.repo, args.version_name))
         else:
-            exit(cls.deploy_indexer(args.env, args.application_version))
+            sys.exit(cls.deploy_indexer(args.env, args.application_version))
 
 
 class IniFileManager:

dcicutils/ecr_scripts.py

@@ -3,6 +3,7 @@ import botocore.exceptions
 import boto3
 import contextlib
 import os
+import sys
 
 from typing import Optional, Union, List
 from .command_utils import yes_or_no
@@ -68,7 +69,7 @@ def ecr_command_context(account_number, ecs_repository=None, ecr_client=None):
             elif account_number != account_number_in_environ:
                 raise RuntimeError("The account number you have specified does not match your declared credentials.")
             yield ECRCommandContext(account_number=account_number, ecs_repository=ecs_repository, ecr_client=ecr_client)
-            exit(0)
+            sys.exit(0)
         except botocore.exceptions.ClientError as e:
             error_info = e.response.get('Error', {})
             message = error_info.get('Message')
@@ -77,12 +78,12 @@ def ecr_command_context(account_number, ecs_repository=None, ecr_client=None):
                 raise RuntimeError("Your security token seems to have expired.")
             elif message:
                 PRINT(f"{code}: {message}")
-                exit(1)
+                sys.exit(1)
             else:
                 raise
     except Exception as e:
         PRINT(f"{full_class_name(e)}: {e}")
-        exit(1)
+        sys.exit(1)
 
 
 class ECRCommandContext:

dcicutils/env_scripts.py

@@ -1,6 +1,7 @@
 import argparse
 import boto3
 import json
+import sys
 import yaml
 
 from .lang_utils import disjoined_list
@@ -52,7 +53,7 @@ def show_global_env_bucket(bucket, mode='json', key=None):
         else:
             PRINT(f"There is no default bucket. Please use a '--bucket' argument"
                   f" to specify one of {disjoined_list(envs_buckets)}.")
-        exit(1)
+        sys.exit(1)
 
     print_heading(bucket, style='=')
 
@@ -70,7 +71,7 @@ def show_global_env_bucket(bucket, mode='json', key=None):
         except Exception as e:
             PRINT("Bucket contents could not be downlaoded.")
             print_error_message(e)
-            exit(1)
+            sys.exit(1)
 
         object = None  # Without this, PyCharm fusses that object might not get set. -kmp 20-Jul-2022
         try:
@@ -78,7 +79,7 @@ def show_global_env_bucket(bucket, mode='json', key=None):
         except Exception as e:
             PRINT("Bucket contents could not be parsed as JSON.")
             print_error_message(e)
-            exit(1)
+            sys.exit(1)
 
         if mode == 'json':
             PRINT(json.dumps(object, indent=2, default=str))
@@ -86,7 +87,7 @@ def show_global_env_bucket(bucket, mode='json', key=None):
             PRINT(yaml.dump(object))
         else:
             PRINT(f"Unknown mode: {mode}. Try 'json' or 'yaml'.")
-            exit(1)
+            sys.exit(1)
 
 
 DEFAULT_BUCKET = get_env_bucket()

dcicutils/license_policies/park-lab-common.jsonc

@@ -248,6 +248,12 @@
             "docutils"  // Used only privately as a separate documentation-generation task for ReadTheDocs
         ],
 
+
+        "GNU General Public License v2 (GPLv2)": [
+            "pyinstaller",
+            "pyinstaller-hooks-contrib"
+        ],
+
         "MIT/X11 Derivative": [
             // The license used by libxkbcommon is complicated and involves numerous included licenses,
             // but all are permissive.

dcicutils/progress_bar.py

@@ -249,7 +249,7 @@ class ProgressBar:
                         if self._interrupt_exit_message:
                             if isinstance(interrupt_exit_message := self._interrupt_exit_message(self), str):
                                 print(interrupt_exit_message)
-                        exit(1)
+                        sys.exit(1)
                     elif interrupt_stop is False or ((interrupt_stop is None) and (self._interrupt_exit is False)):
                         set_interrupt_handler(handle_interrupt)
                         interrupt_continue = self._interrupt_continue(self) if self._interrupt_continue else None

dcicutils/scripts/publish_to_pypi.py

@@ -33,6 +33,7 @@ import argparse
 import os
 import requests
 import subprocess
+import sys
 import toml
 
 from typing import Tuple, Union
@@ -335,7 +336,7 @@ def exit_with_no_action() -> None:
     first prints a message saying no action was taken.
     """
     PRINT("Exiting without taking action.")
-    exit(1)
+    sys.exit(1)
 
 
 PRINT = print

dcicutils/scripts/view_portal_object.py

@@ -201,17 +201,17 @@ def main():
             return
         else:
             _print(f"No PATCH data found in file: {args.patch}")
-            exit(1)
+            sys.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)
+            sys.exit(0)
         else:
             _print(f"{args.uuid}: not found")
-            exit(1)
+            sys.exit(1)
     if args.copy:
         pyperclip.copy(json.dumps(data, indent=4))
     if args.yaml:
@@ -597,18 +597,18 @@ def _print_tree(root_name: Optional[str],
 def _read_json_from_file(file: str) -> Optional[dict]:
     if not os.path.exists(file):
         _print(f"Cannot find file: {file}")
-        exit(1)
+        sys.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)
+                sys.exit(1)
     except Exception as e:
         print(e)
         _print(f"Cannot open file: {file}")
-        exit(1)
+        sys.exit(1)
 
 
 def _print(*args, **kwargs):
@@ -620,7 +620,7 @@ def _print(*args, **kwargs):
 def _exit(message: Optional[str] = None) -> None:
     if message:
         _print(f"ERROR: {message}")
-    exit(1)
+    sys.exit(1)
 
 
 if __name__ == "__main__":

dcicutils/structured_data.py

@@ -57,6 +57,7 @@ class StructuredDataSet:
                  ref_lookup_nocache: bool = False,
                  norefs: bool = False, merge: bool = False,
                  progress: Optional[Callable] = None,
+                 row_reader_hook: Optional[Callable] = None,
                  debug_sleep: Optional[str] = None) -> None:
         self._progress = progress if callable(progress) else None
         self._data = {}
@@ -75,6 +76,7 @@ class StructuredDataSet:
         self._autoadd_properties = autoadd if isinstance(autoadd, dict) and autoadd else None
         self._norefs = True if norefs is True else False
         self._merge = True if merge is True else False  # New merge functionality (2024-05-25)
+        self._row_reader_hook = row_reader_hook if callable(row_reader_hook) else None  # Testing support (2024-06-12)
         self._debug_sleep = None
         if debug_sleep:
             try:
@@ -377,6 +379,8 @@ class StructuredDataSet:
                 structured_row_template = _StructuredRowTemplate(reader.header, schema)
             structured_row = structured_row_template.create_row()
             for column_name, value in row.items():
+                if self._row_reader_hook:
+                    value = self._row_reader_hook(reader.sheet_name, column_name, value)
                 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)

{dcicutils-8.11.0.dist-info → dcicutils-8.11.0.1b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.11.0
+Version: 8.11.0.1b1
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT

{dcicutils-8.11.0.dist-info → dcicutils-8.11.0.1b1.dist-info}/RECORD

@@ -5,7 +5,7 @@ dcicutils/bundle_utils.py,sha256=ZVQcqlt7Yly8-YbL3A-5DW859_hMWpTL6dXtknEYZIw,346
 dcicutils/captured_output.py,sha256=0hP7sPwleMaYXQAvCfJOxG8Z8T_JJYy8ADp8A5ZoblE,3295
 dcicutils/cloudformation_utils.py,sha256=MtWJrSTXyiImgbPHgRvfH9bWso20ZPLTFJAfhDQSVj4,13786
 dcicutils/codebuild_utils.py,sha256=CKpmhJ-Z8gYbkt1I2zyMlKtFdsg7T8lqrx3V5ieta-U,1155
-dcicutils/command_utils.py,sha256=1_h18LGX86sLAkRkH33HNmBkwMb7v2wAh3jL01hzceU,18487
+dcicutils/command_utils.py,sha256=4LkszKXWlvgaUP_7d_tRsRqpOMc9IaohD2Kc9u9bEeU,18506
 dcicutils/common.py,sha256=YE8Mt5-vaZWWz4uaChSVhqGFbFtW5QKtnIyOr4zG4vM,3955
 dcicutils/contribution_scripts.py,sha256=0k5Gw1TumcD5SAcXVkDd6-yvuMEw-jUp5Kfb7FJH6XQ,2015
 dcicutils/contribution_utils.py,sha256=vYLS1JUB3sKd24BUxZ29qUBqYeQBLK9cwo8x3k64uPg,25653
@@ -13,15 +13,15 @@ dcicutils/creds_utils.py,sha256=64BbIfS90T1eJmmQJrDyfrRa3V2F1x7T8lOrEeFfqJY,1112
 dcicutils/data_readers.py,sha256=6EMrY7TjDE8H7bA_TCWtpLQP7slJ0YTL77_dNh6e7sg,7626
 dcicutils/data_utils.py,sha256=k2OxOlsx7AJ6jF-YNlMyGus_JqSUBe4_n1s65Mv1gQQ,3098
 dcicutils/datetime_utils.py,sha256=sM653aw_1zy1qBmfAH-WetCi2Fw9cnFK7FZN_Tg4onI,13499
-dcicutils/deployment_utils.py,sha256=sKv8Jb-_Zw2aH3OAywRlsre-Cqm3a7fEGG3_1PT-r-s,69908
+dcicutils/deployment_utils.py,sha256=6Sv1cM9T944d_9CTJt8O2RPtpw9MiTIPKw_DgYLOnCU,69916
 dcicutils/diff_utils.py,sha256=sQx-yz56DHAcQWOChYbAG3clXu7TbiZKlw-GggeveO0,8118
 dcicutils/docker_utils.py,sha256=30gUiqz7X9rJwSPXTPn4ewjQibUgoSJqhP9o9vn5X-A,1747
-dcicutils/ecr_scripts.py,sha256=cxDl4BQt5W9NN1zjOHYZ7kk3yqoMnaCfNIyLaYmCqdE,19474
+dcicutils/ecr_scripts.py,sha256=puiWqjIshGWNc7ErJvkyizQRINoDToDu7DXHM9ouKMc,19497
 dcicutils/ecr_utils.py,sha256=V1Eif-6THI38W1uKXUyYs-5ciYAVkGLv0sVS4xoh70o,13079
 dcicutils/ecs_utils.py,sha256=1sIIY5IVb__rNyZ5B9iIQKHiUIMldB7JRaeIISLaujY,3590
 dcicutils/env_base.py,sha256=KQmChAvX9riF_khDlW4hmlrHO0GqFMNXrFdiuSmbZtc,6356
 dcicutils/env_manager.py,sha256=Nte1oiW_AQ-isatzsf-fiNpPWInLdfRxzPrATdNoKkI,9444
-dcicutils/env_scripts.py,sha256=0YcEKn7MLLx_St_n74Oe7RlIs7xt3GA0mE04eqrTrfg,3909
+dcicutils/env_scripts.py,sha256=gAoXOemg-zA4I_IPeRuymIfhNOYCw_WmPUa6kcSiWkg,3936
 dcicutils/env_utils.py,sha256=hJTXsn6GC55-55ja1ERBmUbeh-DjJABm74eYRGRaiSc,46970
 dcicutils/env_utils_legacy.py,sha256=J81OAtJHN69o1beHO6q1j7_J6TeblSjnAHlS8VA5KSM,29032
 dcicutils/es_utils.py,sha256=ZksLh5ei7kRUfiFltk8sd2ZSfh15twbstrMzBr8HNw4,7541
@@ -39,7 +39,7 @@ dcicutils/lang_utils.py,sha256=MI3K6bPHLUqlkx3s_9jYZfbGbahiQFlpq4rBE3OYMbg,28151
 dcicutils/license_policies/c4-infrastructure.jsonc,sha256=xEQbIN08Y2xh3gSLRtSz9EhAZox1p3kHC4r678hCpss,278
 dcicutils/license_policies/c4-python-infrastructure.jsonc,sha256=Tkq8P1mKGYlix68I82IFNmasrT4wtSdokOIM-g2B8DQ,296
 dcicutils/license_policies/park-lab-common-server.jsonc,sha256=aaK-NdFDT8f8z_gBXihZnQJ6g3CAZdGSlHOwUP8HvUQ,5790
-dcicutils/license_policies/park-lab-common.jsonc,sha256=0LIFlIQWmdHlt160ku8cTOiB59akgYzRhRN3Xb5G_Aw,18864
+dcicutils/license_policies/park-lab-common.jsonc,sha256=QyzpPveVr87RMpjrLLhnxLSp4VuEWta1gehMAqgKKig,18995
 dcicutils/license_policies/park-lab-gpl-pipeline.jsonc,sha256=vLZkwm3Js-kjV44nug3PizRGDLVnDox4CnvDKu5d2oQ,3260
 dcicutils/license_policies/park-lab-pipeline.jsonc,sha256=9qlY0ASy3iUMQlr3gorVcXrSfRHnVGbLhkS427UaRy4,283
 dcicutils/license_utils.py,sha256=d1cq6iwv5Ju-VjdoINi6q7CPNNL7Oz6rcJdLMY38RX0,46978
@@ -49,7 +49,7 @@ dcicutils/obfuscation_utils.py,sha256=fo2jOmDRC6xWpYX49u80bVNisqRRoPskFNX3ymFAmj
 dcicutils/opensearch_utils.py,sha256=V2exmFYW8Xl2_pGFixF4I2Cc549Opwe4PhFi5twC0M8,1017
 dcicutils/portal_object_utils.py,sha256=Az3n1aL-PQkN5gOFE6ZqC2XkYsqiwKlq7-tZggs1QN4,11062
 dcicutils/portal_utils.py,sha256=R7v4uQUll34mn-NxyU3qoTouAwWrVDzW6W1zBGSU-M4,44762
-dcicutils/progress_bar.py,sha256=UT7lxb-rVF_gp4yjY2Tg4eun1naaH__hB4_v3O85bcE,19468
+dcicutils/progress_bar.py,sha256=R3bWLMYM3Xq9PY7U0JadcFT1m7QmCbrbDp9qs9_Kf_c,19472
 dcicutils/project_utils.py,sha256=qPdCaFmWUVBJw4rw342iUytwdQC0P-XKpK4mhyIulMM,31250
 dcicutils/qa_checkers.py,sha256=cdXjeL0jCDFDLT8VR8Px78aS10hwNISOO5G_Zv2TZ6M,20534
 dcicutils/qa_utils.py,sha256=TT0SiJWiuxYvbsIyhK9VO4uV_suxhB6CpuC4qPacCzQ,160208
@@ -57,14 +57,14 @@ dcicutils/redis_tools.py,sha256=qkcSNMtvqkpvts-Cm9gWhneK523Q_oHwhNUud1be1qk,7055
 dcicutils/redis_utils.py,sha256=VJ-7g8pOZqR1ZCtdcjKz3-6as2DMUcs1b1zG6wSprH4,6462
 dcicutils/s3_utils.py,sha256=LauLFQGvZLfpBJ81tYMikjLd3SJRz2R_FrL1n4xSlyI,28868
 dcicutils/schema_utils.py,sha256=GmRm-XqZKJ6qine16SQF1txcby9WougDav_sYmKNs9E,12400
-dcicutils/scripts/publish_to_pypi.py,sha256=LFzNHIQK2EXFr88YcfctyA_WKEBFc1ElnSjWrCXedPM,13889
+dcicutils/scripts/publish_to_pypi.py,sha256=JCrAiYFF9lMkj3s2w0J2EtN8P65qEamMe3ZZYPCF4Yo,13904
 dcicutils/scripts/run_license_checker.py,sha256=z2keYnRDZsHQbTeo1XORAXSXNJK5axVzL5LjiNqZ7jE,4184
-dcicutils/scripts/view_portal_object.py,sha256=HZzM44BDcGycO9XTOTZyP-F7PRMZaZrnFfiqiT7Qvqg,29777
+dcicutils/scripts/view_portal_object.py,sha256=rnlIoblDpoLPJ-Bor7OHxLgrVZyvqoxA0jmHW8ogg3s,29805
 dcicutils/secrets_utils.py,sha256=8dppXAsiHhJzI6NmOcvJV5ldvKkQZzh3Fl-cb8Wm7MI,19745
 dcicutils/sheet_utils.py,sha256=VlmzteONW5VF_Q4vo0yA5vesz1ViUah1MZ_yA1rwZ0M,33629
 dcicutils/snapshot_utils.py,sha256=ymP7PXH6-yEiXAt75w0ldQFciGNqWBClNxC5gfX2FnY,22961
 dcicutils/ssl_certificate_utils.py,sha256=F0ifz_wnRRN9dfrfsz7aCp4UDLgHEY8LaK7PjnNvrAQ,9707
-dcicutils/structured_data.py,sha256=HVe1ruXz0vH4nRBOwq0cNrfR4KtqocC4U940KRXM5zY,64160
+dcicutils/structured_data.py,sha256=TA7kJ-utVj_xa5XnVs7VaG_XQicl5MUWmrVkDm0N8qE,64471
 dcicutils/submitr/progress_constants.py,sha256=5bxyX77ql8qEJearfHEvsvXl7D0GuUODW0T65mbRmnE,2895
 dcicutils/submitr/ref_lookup_strategy.py,sha256=VJN-Oo0LLna6Vo2cu47eC-eU-yUC9NFlQP29xajejVU,4741
 dcicutils/task_utils.py,sha256=MF8ujmTD6-O2AC2gRGPHyGdUrVKgtr8epT5XU8WtNjk,8082
@@ -73,8 +73,8 @@ dcicutils/trace_utils.py,sha256=g8kwV4ebEy5kXW6oOrEAUsurBcCROvwtZqz9fczsGRE,1769
 dcicutils/validation_utils.py,sha256=cMZIU2cY98FYtzK52z5WUYck7urH6JcqOuz9jkXpqzg,14797
 dcicutils/variant_utils.py,sha256=2H9azNx3xAj-MySg-uZ2SFqbWs4kZvf61JnK6b-h4Qw,4343
 dcicutils/zip_utils.py,sha256=_Y9EmL3D2dUZhxucxHvrtmmlbZmK4FpSsHEb7rGSJLU,3265
-dcicutils-8.11.0.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
-dcicutils-8.11.0.dist-info/METADATA,sha256=fyL2AYscpmbInho84YaFcHMIhk_YTUXPw3MvvmPO9s0,3436
-dcicutils-8.11.0.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
-dcicutils-8.11.0.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
-dcicutils-8.11.0.dist-info/RECORD,,
+dcicutils-8.11.0.1b1.dist-info/LICENSE.txt,sha256=qnwSmfnEWMl5l78VPDEzAmEbLVrRqQvfUQiHT0ehrOo,1102
+dcicutils-8.11.0.1b1.dist-info/METADATA,sha256=v3isC672hWBByXHSDmwdU9yFBEh1wulPulRZ79yyCEs,3440
+dcicutils-8.11.0.1b1.dist-info/WHEEL,sha256=7Z8_27uaHI_UZAc4Uox4PpBhQ9Y5_modZXWMxtUi4NU,88
+dcicutils-8.11.0.1b1.dist-info/entry_points.txt,sha256=51Q4F_2V10L0282W7HFjP4jdzW4K8lnWDARJQVFy_hw,270
+dcicutils-8.11.0.1b1.dist-info/RECORD,,