dcicutils 8.10.0.1b2__tar.gz → 8.11.0__tar.gz

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.10.0.1b2
+Version: 8.11.0
 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-8.10.0.1b2 → dcicutils-8.11.0}/dcicutils/command_utils.py

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

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/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)
-                sys.exit(cls.deploy_new_version(args.env, args.repo, args.version_name))
+                exit(cls.deploy_new_version(args.env, args.repo, args.version_name))
         else:
-            sys.exit(cls.deploy_indexer(args.env, args.application_version))
+            exit(cls.deploy_indexer(args.env, args.application_version))
 
 
 class IniFileManager:

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/dcicutils/ecr_scripts.py

@@ -3,7 +3,6 @@ import botocore.exceptions
 import boto3
 import contextlib
 import os
-import sys
 
 from typing import Optional, Union, List
 from .command_utils import yes_or_no
@@ -69,7 +68,7 @@ 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)
-            sys.exit(0)
+            exit(0)
         except botocore.exceptions.ClientError as e:
             error_info = e.response.get('Error', {})
             message = error_info.get('Message')
@@ -78,12 +77,12 @@ 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}")
-                sys.exit(1)
+                exit(1)
             else:
                 raise
     except Exception as e:
         PRINT(f"{full_class_name(e)}: {e}")
-        sys.exit(1)
+        exit(1)
 
 
 class ECRCommandContext:

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/dcicutils/env_scripts.py

@@ -1,7 +1,6 @@
 import argparse
 import boto3
 import json
-import sys
 import yaml
 
 from .lang_utils import disjoined_list
@@ -53,7 +52,7 @@ 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)}.")
-        sys.exit(1)
+        exit(1)
 
     print_heading(bucket, style='=')
 
@@ -71,7 +70,7 @@ 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)
-            sys.exit(1)
+            exit(1)
 
         object = None  # Without this, PyCharm fusses that object might not get set. -kmp 20-Jul-2022
         try:
@@ -79,7 +78,7 @@ 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)
-            sys.exit(1)
+            exit(1)
 
         if mode == 'json':
             PRINT(json.dumps(object, indent=2, default=str))
@@ -87,7 +86,7 @@ def show_global_env_bucket(bucket, mode='json', key=None):
             PRINT(yaml.dump(object))
         else:
             PRINT(f"Unknown mode: {mode}. Try 'json' or 'yaml'.")
-            sys.exit(1)
+            exit(1)
 
 
 DEFAULT_BUCKET = get_env_bucket()

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/dcicutils/license_policies/park-lab-common.jsonc

@@ -248,12 +248,6 @@
             "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-8.10.0.1b2 → dcicutils-8.11.0}/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)
-                        sys.exit(1)
+                        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-8.10.0.1b2 → dcicutils-8.11.0}/dcicutils/schema_utils.py

@@ -1,5 +1,6 @@
 import os
 from typing import Any, Dict, List, Optional, Tuple
+
 from dcicutils.misc_utils import to_camel_case
 
 
@@ -8,6 +9,7 @@ class JsonSchemaConstants:
     ARRAY = "array"
     BOOLEAN = "boolean"
     DEFAULT = "default"
+    DEPENDENT_REQUIRED = "dependentRequired"
     ENUM = "enum"
     FORMAT = "format"
     INTEGER = "integer"
@@ -29,6 +31,10 @@ class EncodedSchemaConstants:
     LINK_TO = "linkTo"
     MERGE_REF = "$merge"
     MIXIN_PROPERTIES = "mixinProperties"
+    SUBMISSION_COMMENT = "submissionComment"
+    SUBMISSION_EXAMPLES = "submissionExamples"
+    SUBMITTER_REQUIRED = "submitterRequired"
+    SUGGESTED_ENUM = "suggested_enum"
     UNIQUE_KEY = "uniqueKey"
 
 
@@ -203,6 +209,50 @@ def get_description(schema: Dict[str, Any]) -> str:
     return schema.get(SchemaConstants.DESCRIPTION, "")
 
 
+def is_submitter_required(schema: Dict[str, Any]) -> bool:
+    """Return True if the schema is marked as required for submitters.
+
+    Specifically, required for external (i.e. non-admin) submitters.
+
+    This is typically validated within the context of a oneOf, anyOf,
+    or allOf schema on an item type which is used within the team and
+    by external submitters, and is tricky to pick up on automatically.
+    """
+    return schema.get(SchemaConstants.SUBMITTER_REQUIRED, False)
+
+
+def get_submission_comment(schema: Dict[str, Any]) -> str:
+    """Return the submission comment for a property.
+
+    Custom property that can be manually added to a schema to provide
+    additional context for submitters.
+    """
+    return schema.get(SchemaConstants.SUBMISSION_COMMENT, "")
+
+
+def get_submission_examples(schema: Dict[str, Any]) -> List[str]:
+    """Return the submission example for a property.
+
+    Custom property that can be manually added to a schema to provide
+    an example for submitters.
+    """
+    return schema.get(SchemaConstants.SUBMISSION_EXAMPLES, [])
+
+
+def get_suggested_enum(schema: Dict[str, Any]) -> List[str]:
+    """Return the suggested enum for a property.
+
+    Custom property that can be manually added to a schema to provide
+    a suggested list of values for submitters.
+    """
+    return schema.get(SchemaConstants.SUGGESTED_ENUM, [])
+
+
+def get_dependent_required(schema: Dict[str, Any]) -> Dict[str, List[str]]:
+    """Return the dependent required properties of a schema."""
+    return schema.get(SchemaConstants.DEPENDENT_REQUIRED, {})
+
+
 class Schema:
 
     def __init__(self, schema: dict, type: Optional[str] = None) -> None:

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/dcicutils/scripts/publish_to_pypi.py

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

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/dcicutils/scripts/view_portal_object.py

@@ -201,17 +201,17 @@ def main():
             return
         else:
             _print(f"No PATCH data found in file: {args.patch}")
-            sys.exit(1)
+            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")
-            sys.exit(0)
+            exit(0)
         else:
             _print(f"{args.uuid}: not found")
-            sys.exit(1)
+            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}")
-        sys.exit(1)
+        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}")
-                sys.exit(1)
+                exit(1)
     except Exception as e:
         print(e)
         _print(f"Cannot open file: {file}")
-        sys.exit(1)
+        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}")
-    sys.exit(1)
+    exit(1)
 
 
 if __name__ == "__main__":

{dcicutils-8.10.0.1b2 → dcicutils-8.11.0}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.10.0.1b2"  # TODO: To become 8.10.1
+version = "8.11.0"
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"