fix: pin to fastapi>=0.104.1 to pin swagger ui

fixes #337

components/nmdc_runtime/workflow_execution_activity/spec.py

@@ -6,10 +6,11 @@
     WorkflowExecutionActivity,
     Database,
 )
-from pydantic import BaseModel
+from pydantic import BaseModel, ConfigDict
 
 
 class ActivityTree(BaseModel):
+    model_config = ConfigDict(arbitrary_types_allowed=True)
     children: list["ActivityTree"] = []
     data: WorkflowExecutionActivity
     spec: Workflow

nmdc_runtime/api/models/capability.py

@@ -6,7 +6,7 @@
 
 class CapabilityBase(BaseModel):
     name: Optional[str]
-    description: Optional[str]
+    description: Optional[str] = None
 
 
 class Capability(CapabilityBase):

nmdc_runtime/api/models/id.py

@@ -22,11 +22,11 @@
 _base_object_name = f"{_naa}:{_shoulder}{_blade}"
 pattern_base_object_name = re.compile(_base_object_name)
 
-Naa = constr(regex=_naa)
-Shoulder = constr(regex=rf"^{_shoulder}$", min_length=2)
-Blade = constr(regex=_blade, min_length=4)
-AssignedBaseName = constr(regex=_assigned_base_name)
-BaseObjectName = constr(regex=_base_object_name)
+Naa = constr(pattern=_naa)
+Shoulder = constr(pattern=rf"^{_shoulder}$", min_length=2)
+Blade = constr(pattern=_blade, min_length=4)
+AssignedBaseName = constr(pattern=_assigned_base_name)
+BaseObjectName = constr(pattern=_base_object_name)
 
 NameAssigningAuthority = Literal[tuple(NAA_VALUES)]
 
@@ -74,15 +74,15 @@ class IdBindingRequest(BaseModel):
     a: Optional[str]
     v: Any
 
-    @root_validator()
+    @root_validator(skip_on_failure=True)
     def set_or_add_needs_value(cls, values):
         op = values.get("o")
         if op in (IdBindingOp.set, IdBindingOp.addToSet):
             if "v" not in values:
                 raise ValueError("{'set','add'} operations needs value 'v'.")
         return values
 
-    @root_validator()
+    @root_validator(skip_on_failure=True)
     def set_or_add_or_rm_needs_attribute(cls, values):
         op = values.get("o")
         if op in (IdBindingOp.set, IdBindingOp.addToSet, IdBindingOp.rm):

nmdc_runtime/api/models/job.py

@@ -10,7 +10,7 @@
 class JobBase(BaseModel):
     workflow: Workflow
     name: Optional[str]
-    description: Optional[str]
+    description: Optional[str] = None
 
 
 class JobClaim(BaseModel):

nmdc_runtime/api/models/object.py

@@ -37,7 +37,7 @@ class AccessMethod(BaseModel):
     region: Optional[str]
     type: AccessMethodType = AccessMethodType.https
 
-    @root_validator
+    @root_validator(skip_on_failure=True)
     def at_least_one_of_access_id_and_url(cls, values):
         access_id, access_url = values.get("access_id"), values.get("access_url")
         if access_id is None and access_url is None:
@@ -48,7 +48,7 @@ def at_least_one_of_access_id_and_url(cls, values):
 
 
 ChecksumType = constr(
-    regex=rf"(?P<checksumtype>({'|'.join(sorted(hashlib.algorithms_guaranteed))}))"
+    pattern=rf"(?P<checksumtype>({'|'.join(sorted(hashlib.algorithms_guaranteed))}))"
 )
 
 
@@ -57,8 +57,8 @@ class Checksum(BaseModel):
     type: ChecksumType
 
 
-DrsId = constr(regex=r"^[A-Za-z0-9._~\-]+$")
-PortableFilename = constr(regex=r"^[A-Za-z0-9._\-]+$")
+DrsId = constr(pattern=r"^[A-Za-z0-9._~\-]+$")
+PortableFilename = constr(pattern=r"^[A-Za-z0-9._\-]+$")
 
 
 class ContentsObject(BaseModel):
@@ -67,7 +67,7 @@ class ContentsObject(BaseModel):
     id: Optional[DrsId]
     name: PortableFilename
 
-    @root_validator()
+    @root_validator(skip_on_failure=True)
     def no_contents_means_single_blob(cls, values):
         contents, id_ = values.get("contents"), values.get("id")
         if contents is None and id_ is None:
@@ -77,7 +77,7 @@ def no_contents_means_single_blob(cls, values):
 
 ContentsObject.update_forward_refs()
 
-Mimetype = constr(regex=r"^\w+/[-+.\w]+$")
+Mimetype = constr(pattern=r"^\w+/[-+.\w]+$")
 SizeInBytes = conint(strict=True, ge=0)
 
 
@@ -88,7 +88,7 @@ class Error(BaseModel):
 
 class DrsObjectBase(BaseModel):
     aliases: Optional[List[str]]
-    description: Optional[str]
+    description: Optional[str] = None
     mime_type: Optional[Mimetype]
     name: Optional[PortableFilename]
 
@@ -102,7 +102,7 @@ class DrsObjectIn(DrsObjectBase):
     updated_time: Optional[datetime.datetime]
     version: Optional[str]
 
-    @root_validator()
+    @root_validator(skip_on_failure=True)
     def no_contents_means_single_blob(cls, values):
         contents, access_methods = values.get("contents"), values.get("access_methods")
         if contents is None and access_methods is None:

nmdc_runtime/api/models/object_type.py

@@ -8,7 +8,7 @@
 
 class ObjectTypeBase(BaseModel):
     name: Optional[str]
-    description: Optional[str]
+    description: Optional[str] = None
 
 
 class ObjectType(ObjectTypeBase):

nmdc_runtime/api/models/operation.py

@@ -9,7 +9,7 @@
 MetadataT = TypeVar("MetadataT")
 
 
-PythonImportPath = constr(regex=r"^[A-Za-z0-9_.]+$")
+PythonImportPath = constr(pattern=r"^[A-Za-z0-9_.]+$")
 
 
 class OperationError(BaseModel):

nmdc_runtime/api/models/query.py

@@ -141,7 +141,7 @@ class QueryRun(BaseModel):
     result: Optional[Any]
     error: Optional[Any]
 
-    @root_validator
+    @root_validator(skip_on_failure=True)
     def result_xor_error(cls, values):
         result, error = values.get("result"), values.get("error")
         if result is None and error is None:

nmdc_runtime/api/models/workflow.py

@@ -6,7 +6,7 @@
 
 class WorkflowBase(BaseModel):
     name: Optional[str]
-    description: Optional[str]
+    description: Optional[str] = None
     capability_ids: Optional[List[str]]
 
 

nmdc_runtime/site/terminusdb/schema.py

@@ -122,7 +122,7 @@ class NamedThing(DocumentTemplate):
     _key = LexicalKey(["id"])
     _abstract = []
     alternative_identifiers: Set[str]
-    description: Optional[str]
+    description: Optional[str] = None
     id: str
     name: Optional[str]
 
@@ -1105,7 +1105,7 @@ class ImageValue(AttributeValue):
         null
     """
 
-    description: Optional[str]
+    description: Optional[str] = None
     display_order: Optional[str]
     url: Optional[str]
 
@@ -1150,7 +1150,7 @@ class DataObject(NamedThing):
     _key = LexicalKey(["id"])
     compression_type: Optional[str]
     data_object_type: Optional[str]
-    description: Optional[str]
+    description: Optional[str] = None
     file_size_bytes: Optional["xsd:long"]
     md5_checksum: Optional[str]
     name: Optional[str]

requirements/dev.txt

@@ -9,7 +9,7 @@ attrs==23.1.0
     #   -c requirements/main.txt
     #   cattrs
     #   requests-cache
-black==23.9.1
+black==23.10.1
     # via
     #   -c requirements/main.txt
     #   -r requirements/dev.in
@@ -23,7 +23,7 @@ certifi==2023.7.22
     # via
     #   -c requirements/main.txt
     #   requests
-charset-normalizer==3.2.0
+charset-normalizer==3.3.1
     # via
     #   -c requirements/main.txt
     #   requests
@@ -32,7 +32,7 @@ click==8.1.7
     #   -c requirements/main.txt
     #   black
     #   pip-tools
-coverage==7.3.1
+coverage==7.3.2
     # via
     #   -r requirements/dev.in
     #   pytest-cov
@@ -84,7 +84,7 @@ mypy-extensions==1.0.0
     #   black
 nh3==0.2.14
     # via readme-renderer
-packaging==23.1
+packaging==23.2
     # via
     #   -c requirements/main.txt
     #   black
@@ -99,7 +99,7 @@ pip-tools==7.3.0
     # via -r requirements/dev.in
 pkginfo==1.9.6
     # via twine
-platformdirs==3.10.0
+platformdirs==3.11.0
     # via
     #   -c requirements/main.txt
     #   black
@@ -108,7 +108,7 @@ pluggy==1.3.0
     # via
     #   -c requirements/main.txt
     #   pytest
-pycodestyle==2.11.0
+pycodestyle==2.11.1
     # via flake8
 pyflakes==3.1.0
     # via
@@ -121,13 +121,13 @@ pygments==2.16.1
     #   rich
 pyproject-hooks==1.0.0
     # via build
-pytest==7.4.2
+pytest==7.4.3
     # via
     #   -c requirements/main.txt
     #   -r requirements/dev.in
     #   pytest-asyncio
     #   pytest-cov
-pytest-asyncio==0.21.1
+pytest-asyncio==0.22.0
     # via -r requirements/dev.in
 pytest-cov==4.1.0
     # via -r requirements/dev.in
@@ -152,9 +152,9 @@ requests-toolbelt==0.10.1
     #   twine
 rfc3986==2.0.0
     # via twine
-rich==13.5.3
+rich==13.6.0
     # via twine
-setuptools-scm==8.0.3
+setuptools-scm==8.0.4
     # via -r requirements/dev.in
 six==1.16.0
     # via
@@ -183,21 +183,21 @@ url-normalize==1.4.3
     # via
     #   -c requirements/main.txt
     #   requests-cache
-urllib3==1.26.16
+urllib3==1.26.18
     # via
     #   -c requirements/main.txt
     #   requests
     #   requests-cache
     #   twine
-wheel==0.41.2
+wheel==0.41.3
     # via pip-tools
 zipp==3.17.0
     # via
     #   -c requirements/main.txt
     #   importlib-metadata
 
 # The following packages are considered to be unsafe in a requirements file:
-pip==23.2.1
+pip==23.3.1
     # via
     #   -r requirements/dev.in
     #   pip-tools

requirements/main.in

@@ -9,7 +9,7 @@ dagster-graphql
 dagster-postgres
 dependency-injector
 dotted-dict
-fastapi>=0.85.0 # using starlette >=0.20.3 for working colon-containing URL paths.
+fastapi>=0.104.1 # Pins Swagger UI version to 5.9.0 temporarily to handle a bug crashing it in 5.9.1
 fastjsonschema
 fnc
 frozendict