dcicutils 8.13.3__tar.gz → 8.13.3.1b2__tar.gz

{dcicutils-8.13.3 → dcicutils-8.13.3.1b2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: dcicutils
-Version: 8.13.3
+Version: 8.13.3.1b2
 Summary: Utility package for interacting with the 4DN Data Portal and other 4DN resources
 Home-page: https://github.com/4dn-dcic/utils
 License: MIT
@@ -26,8 +26,8 @@ Requires-Dist: PyJWT (>=2.6.0,<3.0.0)
 Requires-Dist: PyYAML (>=6.0.1,<7.0.0)
 Requires-Dist: appdirs (>=1.4.4,<2.0.0)
 Requires-Dist: aws-requests-auth (>=0.4.2,<1)
-Requires-Dist: boto3 (>=1.34.136,<2.0.0)
-Requires-Dist: botocore (>=1.34.136,<2.0.0)
+Requires-Dist: boto3 (>=1.34.147,<2.0.0)
+Requires-Dist: botocore (>=1.34.147,<2.0.0)
 Requires-Dist: chardet (>=5.2.0,<6.0.0)
 Requires-Dist: docker (>=4.4.4,<5.0.0)
 Requires-Dist: elasticsearch (==7.13.4)
@@ -41,7 +41,7 @@ Requires-Dist: pyperclip (>=1.8.2,<2.0.0)
 Requires-Dist: pyramid (==1.10.8)
 Requires-Dist: pytz (>=2020.4)
 Requires-Dist: redis (>=4.5.1,<5.0.0)
-Requires-Dist: requests (>=2.21.0,<3.0.0)
+Requires-Dist: requests (==2.31.0)
 Requires-Dist: rfc3986 (>=1.4.0,<2.0.0)
 Requires-Dist: shortuuid (>=1.0.13,<2.0.0)
 Requires-Dist: structlog (>=19.2.0,<20.0.0)

{dcicutils-8.13.3 → dcicutils-8.13.3.1b2}/dcicutils/common.py

@@ -3,8 +3,7 @@ import os
 import re
 
 from tempfile import TemporaryFile
-from typing import Dict, Union, Tuple, List, Any
-from typing_extensions import Literal
+from typing import Dict, Union, Tuple, List, Any, Literal
 
 
 # ===== Useful constants =====

{dcicutils-8.13.3 → dcicutils-8.13.3.1b2}/dcicutils/qa_checkers.py

@@ -6,8 +6,7 @@ import toml
 import warnings
 
 from collections import defaultdict
-from typing import Optional, List, Dict, Type
-from typing_extensions import Literal
+from typing import Optional, List, Dict, Type, Literal
 from .contribution_utils import Contributions
 from .lang_utils import conjoined_list, n_of, there_are
 from .misc_utils import PRINT, remove_prefix, remove_suffix, getattr_customized, CustomizableProperty

{dcicutils-8.13.3 → dcicutils-8.13.3.1b2}/dcicutils/qa_utils.py

@@ -25,8 +25,7 @@ from botocore.credentials import Credentials as Boto3Credentials
 from botocore.exceptions import ClientError
 from collections import defaultdict
 from json import dumps as json_dumps, loads as json_loads
-from typing import Any, Optional, List, DefaultDict, Union, Type, Dict
-from typing_extensions import Literal
+from typing import Any, Optional, List, DefaultDict, Union, Type, Dict, Literal
 from unittest import mock
 from . import misc_utils as misc_utils_module, command_utils as command_utils_module
 from .common import S3StorageClass

{dcicutils-8.13.3 → dcicutils-8.13.3.1b2}/dcicutils/s3_utils.py

@@ -5,8 +5,7 @@ import mimetypes
 import os
 
 from io import BytesIO
-from typing import Optional, Any, Union
-from typing_extensions import Literal
+from typing import Optional, Any, Union, Literal
 from zipfile import ZipFile
 from .base import get_beanstalk_real_url
 from .common import (

{dcicutils-8.13.3 → dcicutils-8.13.3.1b2}/dcicutils/scripts/view_portal_object.py

@@ -114,16 +114,13 @@ def main():
                         help="Copy object data to clipboard.")
     parser.add_argument("--output", required=False, help="Output file.", type=str)
     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.")
+    parser.add_argument("--summary", action="store_true", required=False, default=False,
+                        help="Summary output (for schema only).")
+    parser.add_argument("--terse", action="store_true", required=False, default=False, help="Terse output.")
     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()
 
-    if args.more_details:
-        args.details = True
-
     portal = _create_portal(ini=args.ini, env=args.env or os.environ.get("SMAHT_ENV"),
                             server=args.server, app=args.app, verbose=args.verbose, debug=args.debug)
 
@@ -143,9 +140,8 @@ def main():
         _output_file = io.open(args.output, "w")
 
     if args.uuid and ((args.uuid.lower() == "schemas") or (args.uuid.lower() == "schema")):
-        _print_all_schema_names(portal=portal, details=args.details,
-                                more_details=args.more_details, all=args.all,
-                                tree=args.tree, raw=args.raw, raw_yaml=args.yaml)
+        _print_all_schema_names(portal=portal, terse=args.terse, all=args.all,
+                                tree=args.tree, summary=args.summary, yaml=args.yaml)
         return
     elif args.uuid and (args.uuid.lower() == "info"):
         if consortia := portal.get_metadata("/consortia?limit=1000"):
@@ -182,7 +178,7 @@ def main():
         if schema:
             if args.copy:
                 pyperclip.copy(json.dumps(schema, indent=4))
-            if not args.raw:
+            if args.summary:
                 if parent_schema_name := _get_parent_schema_name(schema):
                     if schema.get("isAbstract") is True:
                         _print_output(f"{schema_name} | parent: {parent_schema_name} | abstract")
@@ -190,8 +186,8 @@ def main():
                         _print_output(f"{schema_name} | parent: {parent_schema_name}")
                 else:
                     _print_output(schema_name)
-            _print_schema(schema, details=args.details, more_details=args.details,
-                          all=args.all, raw=args.raw, raw_yaml=args.yaml)
+            _print_schema(schema, terse=args.terse,
+                          all=args.all, summary=args.summary, yaml=args.yaml)
             return
 
     data = _get_portal_object(portal=portal, uuid=args.uuid, raw=args.raw, inserts=args.inserts,
@@ -276,9 +272,26 @@ def _get_portal_object(portal: Portal, uuid: str,
             (isinstance(results_type := response.get("@type"), list) and results_type) and
             (isinstance(results_type := results_type[0], str) and results_type.endswith("SearchResults")) and
             (results_type := results_type[0:-len("SearchResults")])):  # noqa
+            # For search results, the type (from XyzSearchResults, above) may not be precisely correct for
+            # each of the results; it may be the supertype (e.g. QualityMetric vs QualityMetricWorkflowRun);
+            # so for types which are supertypes (gotten via Portal.get_schemas_super_type_map) we actually
+            # lookup each result individually to determine its actual precise type.
+            if not ((supertypes := portal.get_schemas_super_type_map()) and (subtypes := supertypes.get(results_type))):
+                subtypes = None
+            response = {}
             for result in results:
                 result.pop("schema_version", None)
-            response = {f"{results_type}": results}
+                if (subtypes and
+                    (result_uuid := result.get("uuid")) and
+                    (individual_result := portal.get_metadata(result_uuid, raise_exception=False)) and
+                    isinstance(result_type:= individual_result.get("@type"), list) and result_type and result_type[0]):  # noqa
+                    result_type = result_type[0]
+                else:
+                    result_type = results_type
+                if response.get(result_type):
+                    response[result_type].append(result)
+                else:
+                    response[result_type] = [result]
         # Get the result as non-raw so we can get its type.
         elif ((response_cooked := portal.get(path, database=database)) and
               (isinstance(response_type := response_cooked.json().get("@type"), list) and response_type)):
@@ -332,19 +345,19 @@ def _get_schema_name_from_schema_named_json_file_name(portal: Portal, value: str
         return False
 
 
-def _print_schema(schema: dict, details: bool = False, more_details: bool = False, all: bool = False,
-                  raw: bool = False, raw_yaml: bool = False) -> None:
-    if raw:
-        if raw_yaml:
+def _print_schema(schema: dict, terse: bool = False, all: bool = False,
+                  summary: bool = False, yaml: bool = False) -> None:
+    if summary is not True:
+        if yaml:
             _print_output(yaml.dump(schema))
         else:
             _print_output(json.dumps(schema, indent=4))
         return
-    _print_schema_info(schema, details=details, more_details=more_details, all=all)
+    _print_schema_info(schema, terse=terse, all=all)
 
 
 def _print_schema_info(schema: dict, level: int = 0,
-                       details: bool = False, more_details: bool = False, all: bool = False,
+                       terse: bool = False, all: bool = False,
                        required: Optional[List[str]] = None) -> None:
     if not schema or not isinstance(schema, dict):
         return
@@ -396,7 +409,7 @@ def _print_schema_info(schema: dict, level: int = 0,
                     _print_output(f"  - {reference_property['name']}: {reference_property['ref']}")
         if schema.get("additionalProperties") is True:
             _print_output(f"  - additional properties are allowed")
-    if not more_details:
+    if terse:
         return
     if properties := (schema.get("properties") if level == 0 else schema):
         if level == 0:
@@ -422,8 +435,7 @@ def _print_schema_info(schema: dict, level: int = 0,
                     if property.get("calculatedProperty"):
                         suffix += f" | calculated"
                     _print_output(f"{spaces}- {property_name}: {property_type}{suffix}")
-                    _print_schema_info(object_properties, level=level + 1,
-                                       details=details, more_details=more_details, all=all,
+                    _print_schema_info(object_properties, level=level + 1, terse=terse, all=all,
                                        required=property.get("required"))
                 elif property_type == "array":
                     suffix = ""
@@ -447,7 +459,7 @@ def _print_schema_info(schema: dict, level: int = 0,
                                 suffix = ""
                                 _print_output(f"{spaces}- {property_name}: array of object{suffix}")
                                 _print_schema_info(property_items.get("properties"), level=level + 1,
-                                                   details=details, more_details=more_details, all=all,
+                                                   terse=terse, all=all,
                                                    required=property_items.get("required"))
                             elif property_type == "array":
                                 # This (array-of-array) never happens to occur at this time (February 2024).
@@ -523,13 +535,13 @@ def _print_schema_info(schema: dict, level: int = 0,
 
 
 def _print_all_schema_names(portal: Portal,
-                            details: bool = False, more_details: bool = False, all: bool = False,
-                            tree: bool = False, raw: bool = False, raw_yaml: bool = False) -> None:
+                            terse: bool = False, all: bool = False,
+                            tree: bool = False, summary: bool = False, yaml: bool = False) -> None:
     if not (schemas := _get_schemas(portal)):
         return
 
-    if raw:
-        if raw_yaml:
+    if summary is not True:
+        if yaml:
             _print_output(yaml.dump(schemas))
         else:
             _print_output(json.dumps(schemas, indent=4))
@@ -550,8 +562,8 @@ def _print_all_schema_names(portal: Portal,
                 _print_output(f"{schema_name} | abstract")
             else:
                 _print_output(schema_name)
-        if details:
-            _print_schema(schemas[schema_name], details=details, more_details=more_details, all=all)
+        if not terse:
+            _print_schema(schemas[schema_name], terse=terse, all=all)
 
 
 def _get_parent_schema_name(schema: dict) -> Optional[str]:

{dcicutils-8.13.3 → dcicutils-8.13.3.1b2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "dcicutils"
-version = "8.13.3"
+version = "8.13.3.1b2"  # TODO: To become 8.13.4
 description = "Utility package for interacting with the 4DN Data Portal and other 4DN resources"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -39,8 +39,8 @@ classifiers = [
 
 [tool.poetry.dependencies]
 python = ">=3.8.1,<3.13"
-boto3 = "^1.34.136"
-botocore = "^1.34.136"
+boto3 = "^1.34.147"
+botocore = "^1.34.147"
 # 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"
@@ -63,7 +63,7 @@ pyperclip = "^1.8.2"
 PyYAML = "^6.0.1"
 # N.B. 2024-06-30: Updating (via poetry update) from requests 2.31.0 (2023-05-22)
 # to 2.32.3 (2024-05-29) causes utils GA/CI to fail (on test_ecr_utils_workflow) for some reason.
-requests = "^2.21.0"
+requests = "2.31.0"
 rfc3986 = "^1.4.0"
 shortuuid = "^1.0.13"
 structlog = "^19.2.0"
@@ -75,8 +75,8 @@ webtest = "^2.0.34"
 
 
 [tool.poetry.dev-dependencies]
-boto3-stubs = "^1.34.136"
-botocore-stubs = "^1.34.136"
+boto3-stubs = "^1.34.147"
+botocore-stubs = "^1.34.147"
 coverage = "^7.5.4"
 # 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