UncountablePythonSDK 0.0.16__py3-none-any.whl → 0.0.18__py3-none-any.whl

pkgs/type_spec/util.py

@@ -1,7 +1,7 @@
 import json
 import os
 from dataclasses import dataclass
-from typing import Dict, List, Optional, TypeVar, Union
+from typing import Optional, TypeVar, Union
 
 import regex as re
 
@@ -29,11 +29,11 @@ LiteralTypeValue = Union[str, bool]
 class ParsedTypePart:
     name: str
     # An empty list is distinct from None
-    parameters: Optional[List["ParsedTypePath"]] = None
+    parameters: Optional[list["ParsedTypePath"]] = None
     literal_value: Optional[LiteralTypeValue] = None
 
 
-ParsedTypePath = List[ParsedTypePart]
+ParsedTypePath = list[ParsedTypePart]
 
 
 @dataclass
@@ -48,7 +48,7 @@ def consume_parameter(
 ) -> ConsumedParameter:
     if bits[at] != "'":
         return ConsumedParameter(at=at, part=ParsedTypePart(name=bits[at]))
-    quote_stack: List[str] = []
+    quote_stack: list[str] = []
     at += 1
     while at < len(bits):
         if bits[at] == "'":
@@ -68,7 +68,7 @@ def parse_type_str(type_str: str) -> ParsedTypePath:
     """
     IMPROVE: will not detect all errors yet, focuses on correct cases
     """
-    raw_bits: List[str] = re.split(r"([.<>,'])", type_str)
+    raw_bits: list[str] = re.split(r"([.<>,'])", type_str)
     bits = [
         stripped_bit
         for stripped_bit in (padded_bit.strip() for padded_bit in raw_bits)
@@ -81,7 +81,7 @@ def parse_type_str(type_str: str) -> ParsedTypePath:
     cur_path = result
     cur_path.append(cur_part)
 
-    path_stack: List[ParsedTypePath] = []
+    path_stack: list[ParsedTypePath] = []
 
     at = 1
     while at < len(bits):
@@ -156,19 +156,19 @@ def is_valid_property_name(name: str) -> bool:
     return re_pattern_property_name.match(name) is not None
 
 
-def check_fields(data: Dict[str, T], allowed: List[str]) -> None:
+def check_fields(data: dict[str, T], allowed: list[str]) -> None:
     for key in data:
         if key not in allowed:
             raise Exception(f"unexpected-field: {key}")
 
 
-def split_any_name(name: str) -> List[str]:
+def split_any_name(name: str) -> list[str]:
     """
     Splits a name on case and underscores.
     myName => [my, name]
     my_name => [my, name]
     """
-    bits: List[str] = re_pattern_split_name.split(name)
+    bits: list[str] = re_pattern_split_name.split(name)
     return [s.lower() for s in filter(lambda x: x is not None and x != "_", bits)]
 
 

pkgs/type_spec/value_spec/__main__.py

@@ -17,7 +17,7 @@ If null is allowed as a legitimate value, such as in conditionals like `if`, the
 """
 
 import sys
-from typing import Type, TypeVar, cast
+from typing import TypeVar, cast
 
 import regex as re
 import yaml
@@ -177,7 +177,7 @@ def main() -> None:
             raise Exception(f"missing-{key}:{get_where()}")
         return cast(base_t.PureJsonValue, x)
 
-    def get_as(node: base_t.PureJsonValue, key: str, type_: Type[TypeT]) -> TypeT:
+    def get_as(node: base_t.PureJsonValue, key: str, type_: type[TypeT]) -> TypeT:
         raw = get(node, key)
         assert isinstance(raw, type_)
 

pkgs/type_spec/value_spec/emit_python.py

@@ -22,6 +22,7 @@ def emit_functions(functions: list[value_spec_t.Function]) -> str:
     out.write(
         f"""{MODIFY_NOTICE}
 {LINT_HEADER}
+import datetime
 from typing import cast, Union
 
 from decimal import Decimal

type_spec/external/api/batch/execute_batch_load_async.yaml

@@ -0,0 +1,18 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/batch/execute_batch_load_async
+    function: main.site.app.external.batch.execute_batch_load_async.execute_batch_load_async
+    desc: Run multiple API calls via one request
+
+Arguments:
+    type: Object
+    properties:
+        requests:
+            type: List<async_batch.AsyncBatchRequest>
+
+Data:
+    type: Object
+    properties:
+      job_id: 
+        type: ObjectId

type_spec/external/api/chemical/convert_chemical_formats.yaml

@@ -0,0 +1,33 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/chemical/convert_chemical_formats
+    function: main.site.app.external.chemical.convert_chemical_formats.convert_chemical_formats
+    desc: Converts chemical formats, into the format used by Uncountable and usable in other APIs for eg. set_input_attribute_values
+
+
+ChemicalStructureFile:
+    type: Object
+    properties:
+        struct_file:
+            type: String
+            desc: Stringified chemical structure. MOL v2000/3000, SMILES, Part of SDF.
+
+Arguments:
+    type: Object
+    properties:
+        source_chemical_structures:
+            type: List<ChemicalStructureFile>
+
+UncountableChemicalStructure:
+    type: Alias
+    alias: Dict<String, JsonValue>
+    desc: Uncountable format for chemical structures compatible with set ingredient attributes api etc.
+
+Data:
+    type: Object
+    properties:
+        chemical_structures:
+            type: List<UncountableChemicalStructure>
+            desc: The parsed chemical structures in the Uncountable format
+            convert_value: no_convert

type_spec/external/api/entity/create_entities.yaml

@@ -19,7 +19,7 @@ Arguments:
             type: ObjectId
             desc: "Definition id for the entities to create"
         entity_type:
-            type: Union<Literal<entity.EntityType.lab_request>, Literal<entity.EntityType.approval>, Literal<entity.EntityType.custom_entity>, Literal<entity.EntityType.task>, Literal<entity.EntityType.project>>
+            type: Union<Literal<entity.EntityType.lab_request>, Literal<entity.EntityType.approval>, Literal<entity.EntityType.custom_entity>, Literal<entity.EntityType.task>, Literal<entity.EntityType.project>, Literal<entity.EntityType.equipment>, Literal<entity.EntityType.inv_local_locations>>
             desc: "The type of the entities to create"
         entities_to_create:
             type: List<EntityToCreate>

type_spec/external/api/entity/create_entity.yaml

@@ -26,7 +26,7 @@ Arguments:
             type: ObjectId
             desc: "Definition id of the entity to create"
         entity_type:
-            type: Union<Literal<entity.EntityType.lab_request>, Literal<entity.EntityType.approval>, Literal<entity.EntityType.custom_entity>, Literal<entity.EntityType.task>, Literal<entity.EntityType.project>>
+            type: Union<Literal<entity.EntityType.lab_request>, Literal<entity.EntityType.approval>, Literal<entity.EntityType.custom_entity>, Literal<entity.EntityType.task>, Literal<entity.EntityType.project>, Literal<entity.EntityType.equipment>, Literal<entity.EntityType.inv_local_locations>>
             desc: "The type of the entities requested"
         field_values?:
             type: Optional<List<field_values.FieldRefNameValue>>

type_spec/external/api/id_source/list_id_source.yaml

@@ -0,0 +1,35 @@
+$endpoint:
+    is_sdk: true
+    method: get
+    path: ${external}/id_source/list_id_source
+    function: main.site.app.external.id_source.list_id_source.list_id_source
+    desc: "Lists id and label pairs"
+Arguments:
+    type: Object
+    properties:
+        spec:
+            type: id_source.IdSourceSpec
+            desc: "The id source spec to use"
+        search_label:
+            type: String
+            desc: Text to search within the labels to search matches
+        offset?:
+            type: Optional<Integer>
+            desc: "Used for pagination. Pagination is done based on the sorting of the config"
+        limit?:
+            type: Optional<Integer>
+            desc: "The number of data points to return. If not filled in, it will be set to 100, and cannot be set higher than 100"
+
+IdName:
+    type: Object
+    properties:
+        id:
+            type: Union<ObjectId,String>
+        name:
+            type: String
+
+Data:
+    type: Object
+    properties:
+        results:
+            type: List<IdName>

type_spec/external/api/id_source/match_id_source.yaml

@@ -0,0 +1,32 @@
+$endpoint:
+    is_sdk: true
+    method: get
+    path: ${external}/id_source/match_id_source
+    function: main.site.app.external.id_source.match_id_source.match_id_source
+    desc: "Lists id and label pairs"
+Arguments:
+    type: Object
+    properties:
+        spec:
+            type: id_source.IdSourceSpec
+            desc: "The id source spec to use"
+        names:
+            type: List<String>
+            desc: "The names to match with the id source.  At most 10 are allowed at a time"
+
+Match:
+    type: Object
+    properties:
+        name:
+            type: String
+            desc: The name used to match
+        ids:
+            type: List<Union<ObjectId, String>>
+            desc: The list of matches
+
+Data:
+    type: Object
+    properties:
+        results:
+            type: List<Match>
+            convert_value: no_convert

type_spec/external/api/recipe_links/create_recipe_link.yaml

@@ -0,0 +1,25 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/recipe_links/create_recipe_link
+    function: main.site.app.external.recipe_links.create_recipe_link.create_recipe_link
+    desc: Create a link between two recipes.  Skip if the link already exists
+
+Arguments:
+    type: Object
+    properties:
+        recipe_from_key:
+            type: identifier.IdentifierKey
+            desc: "Identifier for the recipe the link comes from"
+        recipe_to_key:
+            type: identifier.IdentifierKey
+            desc: "Identifier for the recipe the link goes to"
+        link_type:
+            type: Union<Literal<recipe_links.RecipeLinkType.child>, Literal<recipe_links.RecipeLinkType.control>, Literal<recipe_links.RecipeLinkType.user_link>>
+            desc: "The type of link being created"
+        name:
+            type: String
+            desc: "The name used for the link"
+
+Data:
+  type: async_batch.AsyncBatchActionReturn

type_spec/external/api/recipes/associate_recipe_as_input.yaml

@@ -0,0 +1,19 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/recipes/associate_recipe_as_input
+    function: main.site.app.external.recipes.associate_recipe_as_input.associate_recipe_as_input
+    desc: Create or return the input association for a recipe
+
+Arguments:
+    type: Object
+    properties:
+        recipe_key:
+            type: identifier.IdentifierKey
+            desc: "Identifier for the recipe"
+
+Data:
+  type: Object
+  properties:
+    result_id:
+      type: ObjectId

type_spec/external/api/recipes/associate_recipe_as_lot.yaml

@@ -0,0 +1,19 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/recipes/associate_recipe_as_lot
+    function: main.site.app.external.recipes.associate_recipe_as_lot.associate_recipe_as_lot
+    desc: Create a new lot association for the provided recipe with the provided ingredient
+
+Arguments:
+    type: Object
+    properties:
+        recipe_key:
+            type: identifier.IdentifierKey
+            desc: "Identifier for the recipe"
+        ingredient_key:
+            type: identifier.IdentifierKey
+            desc: "Identifier for the ingredient"
+
+Data:
+  type: async_batch.AsyncBatchActionReturn

type_spec/external/api/recipes/create_recipe.yaml

@@ -0,0 +1,38 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/recipes/create_recipe
+    function: main.site.app.external.recipes.create_recipe.create_recipe
+    desc: Returns the id of the recipe being created.
+
+
+Arguments:
+    type: Object
+    properties:
+        name?:
+            type: String
+            desc: The name for the recipe
+        material_family_id:
+            type: ObjectId
+            desc: The material family for the recipe
+        workflow_id:
+            type: ObjectId
+            desc: The identifier of the workflow to create the recipe with
+        workflow_variant_id?:
+            type: Optional<ObjectId>
+            desc: The identifier of the workflow variant to create the recipe with
+        recipe_metadata?:
+            type: List<recipe_metadata.MetadataValue>
+            desc: Metadata values to populate the recipe with
+        identifiers:
+            type: recipe_identifiers.RecipeIdentifiers
+            desc: A recipe won't be created if it matches the identifier.  An identifier must be unique in the schema
+        definition_key?:
+            type: identifier.IdentifierKey
+            desc: The entity definition identifier, default is used if not supplied
+
+Data:
+  type: Object
+  properties:
+    result_id:
+      type: ObjectId

type_spec/external/api/recipes/get_recipes_data.yaml

@@ -3,7 +3,7 @@ $endpoint:
     method: get
     path: ${external}/recipes/external_get_recipes_data
     function: main.site.app.external.recipes.get_recipes_data.get_recipes_data
-    desc: "Gets all data associated with a set of recipes / experiments. Because Uncountables recipe structure is complex, various data values are exploded out to increase efficiency in parsing, and this page is paginated to prevent too large of return values"
+    desc: "Gets all data associated with a set of recipes. Because Uncountables recipe structure is complex, various data values are exploded out to increase efficiency in parsing, and this page is paginated to prevent too large of return values"
 Arguments:
     type: Object
     properties:
@@ -22,7 +22,7 @@ Arguments:
 
 RecipeOutput:
     type: Object
-    desc: "A representation of a single measurement associated with a recipe / experiment within Uncountable system"
+    desc: "A representation of a single measurement associated with a recipe within Uncountable system"
     properties:
         id:
             type: ObjectId
@@ -113,7 +113,7 @@ RecipeStep:
             desc: "An optional name for the recipe step"
         recipe_step_id:
             type: ObjectId
-            desc: "An ID value for the recipe step, used elsewhere to reference the part of the recipe / experiment that the input was placed in"
+            desc: "An ID value for the recipe step, used elsewhere to reference the part of the recipe that the input was placed in"
         recipe_step_number:
             type: Integer
             desc: "An ordering for the recipe step, allowing the user to determine the ordering of the steps"
@@ -126,24 +126,24 @@ RecipeStepGroup:
     properties:
         name:
             type: Optional<String>
-            desc: "An optional name for the recipe step group. These names are on a per recipe basis, allowing users to individually name sub-components of recipes / experiments"
+            desc: "An optional name for the recipe step group. These names are on a per recipe basis, allowing users to individually name sub-components of recipes"
         recipe_steps:
             type: List<RecipeStep>
-            desc: "A listing of recipe steps. Recipe Steps are the base component in Uncountables recipe structure, where inputs are directly placed"
+            desc: "A listing of recipe steps. Recipe Steps are the base component in Uncountable's recipe structure, where inputs are directly placed"
 
 RecipeWorkflowStep:
     type: Object
-    desc: "A workflow step associated with a recipe / experiment. Workflow steps are comprised of recipe step groups, in turn comprised of recipe steps, where inputs are located. These groupings exists to give customers the ability to flexibly place inputs into the correct process ordering"
+    desc: "A workflow step associated with a recipe. Workflow steps are comprised of recipe step groups, in turn comprised of recipe steps, where inputs are located. These groupings exists to give customers the ability to flexibly place inputs into the correct process ordering"
     properties:
         recipe_workflow_step_id:
             type: ObjectId
             desc: "A unique reference for the workflow step within the recipe."
         workflow_step_id:
             type: ObjectId
-            desc: "A reference to the workflow_step_id for the workflow. This will be shared across recipes / experiments, and can be used to do analysis about what part of a generic process inputs are located in."
+            desc: "A reference to the workflow_step_id for the workflow. This will be shared across recipes, and can be used to do analysis about what part of a generic process inputs are located in."
         recipe_step_groups:
             type: List<RecipeStepGroup>
-            desc: "A listing of recipe step groups within the recipe / experiment"
+            desc: "A listing of recipe step groups within the recipe"
 
 RecipeStepRelationship:
     type: Object
@@ -172,46 +172,46 @@ Recipe:
     properties:
         recipe_id:
             type: ObjectId
-            desc: "A unique identifier for the recipe / experiment. Used for joining elsewhere"
+            desc: "A unique identifier for the recipe. Used for joining elsewhere"
         creating_user_id?:
             type: ObjectId
-            desc: "The user ID who originally created the recipe / experiment. Null when created from automated scripts, such as data transfers, or from the Uncountable implementation team."
+            desc: "The user ID who originally created the recipe. Null when created from automated scripts, such as data transfers, or from the Uncountable implementation team."
         create_datetime:
             type: String
-            desc: "When the recipe / experiment was created"
+            desc: "When the recipe was created"
         last_modified_datetime:
             type: String
-            desc: "when the recipe / experiment was last modified"
+            desc: "when the recipe was last modified"
         name:
             type: String
-            desc: "The full name in the system of the recipe / experiment"
+            desc: "The full name in the system of the recipe"
         notes:
             type: Optional<String>
-            desc: "Any notes associated with the recipe / experiment. This may be null if there are no notes present"
+            desc: "Any notes associated with the recipe. This may be null if there are no notes present"
         barcode_value?:
             type: String
             desc: "The value used in the barcoding system to lookup this experiment."
         workflow_id:
             type: ObjectId
-            desc: "The workflow ID associated with the recipe / experiment. Workflows correspond to a set of experimental steps performed, and are referenced in the workflows return object"
+            desc: "The workflow ID associated with the recipe. Workflows correspond to a set of experimental steps performed, and are referenced in the workflows return object"
         metadata:
             type: List<recipe_metadata.RecipeMetadata>
-            desc: "Metadata associated with a recipe / experimen. Metadata includes values that are neither ingredients nor process parameters, such as a location of an experiment"
+            desc: "Metadata associated with a recipe. Metadata includes values that are neither ingredients nor process parameters, such as a location of an experiment"
         inputs:
             type: List<RecipeInput>
-            desc: "Inputs and quantities of those inputs associated with a recipe / experimen. Uncountable refers to inputs as either ingredients or process parameters."
+            desc: "Inputs and quantities of those inputs associated with a recipe. Uncountable refers to inputs as either ingredients or process parameters."
         outputs:
             type: List<RecipeOutput>
-            desc: "Outputs and quantities of those outputs associated with a recipe / experimen. These can be of any form referred to in the Uncountable system."
+            desc: "Outputs and quantities of those outputs associated with a recipe. These can be of any form referred to in the Uncountable system."
         workflow_steps:
             type: List<RecipeWorkflowStep>
-            desc: "A reference of workflow steps in the recipe / experimen. This is used to reference input values to where they occurred in the experimental process."
+            desc: "A reference of workflow steps in the recipe. This is used to reference input values to where they occurred in the experimental process."
         tag_ids:
             type: List<ObjectId>
-            desc: A list of Tag IDs associated with the recipe / experiment
+            desc: A list of Tag IDs associated with the recipe
         experiment_group_ids:
             type: List<ObjectId>
-            desc: A list of experiment group IDs associated with the recipe / experiment
+            desc: A list of experiment group IDs associated with the recipe
         step_relationships:
             type: List<RecipeStepRelationship>
 

type_spec/external/api/recipes/set_recipe_inputs.yaml

@@ -25,6 +25,12 @@ RecipeInputValue:
         set_actual_value?:
             type: Boolean
             desc: "If True, modify the actual value for the input. If not provided or False, modify the set value for the input."
+        lot_recipe_id?:
+            type: ObjectId
+            desc: The recipe id for a lot to be associated to this recipe input. If the recipe is not a lot, it will be created as a lot.
+        remove?:
+            type: Boolean
+            desc: When true will remove the input from the recipe
 
 Arguments:
     type: Object

type_spec/external/api/recipes/set_recipe_metadata.yaml

@@ -0,0 +1,19 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/recipes/set_recipe_metadata
+    function: main.site.app.external.recipes.set_recipe_metadata.set_recipe_metadata
+    desc: "Set metadata values on a recipe"
+
+Arguments:
+    type: Object
+    properties:
+        recipe_key:
+            type: identifier.IdentifierKey
+            desc: "Identifier for the recipe"
+        recipe_metadata:
+            type: List<recipe_metadata.MetadataValue>
+            desc: "Metadata values to populate the recipe with"
+
+Data:
+  type: Object

type_spec/external/api/triggers/run_trigger.yaml

@@ -0,0 +1,18 @@
+$endpoint:
+    is_sdk: true
+    method: post
+    path: ${external}/triggers/run_trigger
+    function: main.site.app.external.triggers.run_trigger.run_trigger
+    desc: "Runs a trigger.  Requires admin access"
+
+Arguments:
+    type: Object
+    properties:
+        entity?:
+            type: entity.Entity
+        trigger_ref_name:
+            type: String
+
+Data:
+    type: response.Response
+    properties:

uncountable/core/client.py

@@ -1,15 +1,15 @@
+import base64
+import json
+import typing
 from dataclasses import dataclass
 from enum import StrEnum
-import json
 from urllib.parse import urljoin
-import base64
-import typing
+
 import requests
-from uncountable.types.base import JsonValue
-from uncountable.types.client_base import APIRequest, ClientMethods
+
 from pkgs.argument_parser import CachedParser
 from pkgs.serialization_util import serialize_for_api
-
+from uncountable.types.client_base import APIRequest, ClientMethods
 
 DT = typing.TypeVar("DT")
 
@@ -24,8 +24,8 @@ class HTTPRequestBase:
     method: EndpointMethod
     url: str
     headers: dict[str, str]
-    body: typing.Optional[str] = None
-    query_params: typing.Optional[dict[str, str]]
+    body: typing.Optional[typing.Union[str, dict[str, str]]] = None
+    query_params: typing.Optional[dict[str, str]] = None
 
 
 @dataclass(kw_only=True)
@@ -37,6 +37,7 @@ class HTTPGetRequest(HTTPRequestBase):
 @dataclass(kw_only=True)
 class HTTPPostRequest(HTTPRequestBase):
     method: typing.Literal[EndpointMethod.POST]
+    body: typing.Union[str, dict[str, str]]
 
 
 HTTPRequest = HTTPPostRequest | HTTPGetRequest
@@ -98,9 +99,7 @@ class Client(ClientMethods):
         match self._auth_details:
             case AuthDetailsApiKey():
                 encoded = base64.standard_b64encode(
-                    f"{self._auth_details.api_id}:{self._auth_details.api_secret_key}".encode(
-                        "utf-8"
-                    )
+                    f"{self._auth_details.api_id}:{self._auth_details.api_secret_key}".encode()
                 ).decode("utf-8")
                 return {"Authorization": f"Basic {encoded}"}
         typing.assert_never(self._auth_details)
@@ -108,21 +107,21 @@ class Client(ClientMethods):
     def _build_http_request(self, *, api_request: APIRequest) -> HTTPRequest:
         headers = self._build_auth_headers()
         method = api_request.method.lower()
-        query_params = {"data": json.dumps(serialize_for_api(api_request.args))}
+        data = {"data": json.dumps(serialize_for_api(api_request.args))}
         match method:
             case "get":
                 return HTTPGetRequest(
                     method=EndpointMethod.GET,
                     url=urljoin(self._base_url, api_request.endpoint),
-                    query_params=query_params,
+                    query_params=data,
                     headers=headers,
                 )
             case "post":
                 return HTTPPostRequest(
                     method=EndpointMethod.POST,
                     url=urljoin(self._base_url, api_request.endpoint),
+                    body=data,
                     headers=headers,
-                    query_params=query_params
                 )
             case _:
                 raise ValueError(f"unsupported request method: {method}")