Fetaure fds 829 component requirements

apps/schematic/api/.gitignore

@@ -71,6 +71,8 @@ target/
 *secrets*
 synapse_config.yaml
 schematic_service_account_creds.json
+private_localhost_certificate.crt
+private_localhost.key
 
 #schematic downloaded files
 manifests

apps/schematic/api/.openapi-generator/FILES

@@ -13,6 +13,9 @@ schematic_api/models/__init__.py
 schematic_api/models/asset_type.py
 schematic_api/models/base_model_.py
 schematic_api/models/basic_error.py
+schematic_api/models/component_requirement_array.py
+schematic_api/models/component_requirement_graph.py
+schematic_api/models/component_requirement_subgraph.py
 schematic_api/models/connected_node_pair.py
 schematic_api/models/connected_node_pair_array.py
 schematic_api/models/connected_node_pair_page.py

apps/schematic/api/schematic_api/controllers/manifest_generation_controller.py

@@ -17,8 +17,8 @@ def generate_google_sheet_manifests(
     manifest_title=None,
     data_type_array=None,
     display_label_type=None,
-    asset_view_id=None,
     use_strict_validation=None,
+    asset_view_id=None,
     generate_all_manifests=None,
 ):  # noqa: E501
     """Generates a list of google sheet links
@@ -37,10 +37,10 @@ def generate_google_sheet_manifests(
     :type data_type_array: List[str]
     :param display_label_type: The type of label to display
     :type display_label_type: str
-    :param asset_view_id: ID of view listing all project data assets. E.g. for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project
-    :type asset_view_id: str
     :param use_strict_validation: If true, users are blocked from entering incorrect values. If false, users will get a warning when using incorrect values.
     :type use_strict_validation: bool
+    :param asset_view_id: ID of view listing all project data assets. E.g. for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project
+    :type asset_view_id: str
     :param generate_all_manifests: If true, a manifest for all components will be generated, datasetIds will be ignored. If false, manifests for each id in datasetIds will be generated.
     :type generate_all_manifests: bool
 
@@ -53,7 +53,7 @@ def generate_google_sheet_manifests(
         manifest_title,
         data_type_array,
         display_label_type,
-        asset_view_id,
         use_strict_validation,
+        asset_view_id,
         generate_all_manifests,
     )

apps/schematic/api/schematic_api/controllers/manifest_generation_controller_impl.py

@@ -11,7 +11,6 @@
     handle_exceptions,
     get_access_token,
     download_schema_file_as_jsonld,
-    InvalidValueError,
 )
 
 
@@ -22,10 +21,10 @@ def generate_google_sheet_manifests(
     dataset_id_array: list[str] | None,
     manifest_title: str | None,
     data_type_array: list[str] | None,
-    display_label_type: DisplayLabelType = "class_label",
-    asset_view_id: str | None = None,
-    use_strict_validation: bool = True,
-    generate_all_manifests: bool = False,
+    display_label_type: DisplayLabelType,
+    use_strict_validation: bool,
+    asset_view_id: str | None,
+    generate_all_manifests: bool,
 ) -> tuple[GoogleSheetLinks | BasicError, int]:
     """Generates a list of links to manifests in google sheet form
 
@@ -57,38 +56,9 @@ def generate_google_sheet_manifests(
     """
 
     if generate_all_manifests:
-        if dataset_id_array:
-            raise InvalidValueError(
-                "When generate_all_manifests is True dataset_id_array must be None",
-                {"dataset_id_array": dataset_id_array},
-            )
-        if data_type_array:
-            raise InvalidValueError(
-                "When generate_all_manifests is True data_type_array must be None",
-                {"data_type_array": data_type_array},
-            )
         data_type_array = ["all manifests"]
-
-    else:
-        if not data_type_array:
-            raise InvalidValueError(
-                (
-                    "When generate_all_manifests is False data_type_array must be a list with "
-                    "at least one item"
-                ),
-                {"data_type_array": data_type_array},
-            )
-        if dataset_id_array and len(dataset_id_array) != len(data_type_array):
-            raise InvalidValueError(
-                (
-                    "When generate_all_manifests is False data_type_array and dataset_id_array "
-                    "must both lists with the same length"
-                ),
-                {
-                    "data_type_array": data_type_array,
-                    "dataset_id_array": dataset_id_array,
-                },
-            )
+    if not data_type_array:
+        data_type_array = []
 
     access_token = get_access_token()
     if asset_view_id:

apps/schematic/api/schematic_api/controllers/schema_controller.py

@@ -5,6 +5,12 @@
 from typing import Union
 
 from schematic_api.models.basic_error import BasicError  # noqa: E501
+from schematic_api.models.component_requirement_array import (
+    ComponentRequirementArray,
+)  # noqa: E501
+from schematic_api.models.component_requirement_graph import (
+    ComponentRequirementGraph,
+)  # noqa: E501
 from schematic_api.models.connected_node_pair_array import (
     ConnectedNodePairArray,
 )  # noqa: E501
@@ -42,6 +48,48 @@ def get_component(
     )
 
 
+def get_component_requirements_array(
+    component_label, schema_url, display_label_type=None
+):  # noqa: E501
+    """Given a source model component (see https://w3id.org/biolink/vocab/category for definnition of component), return all components required by it in array form.
+
+    Given a source model component (see https://w3id.org/biolink/vocab/category for definnition of component), return all components required by it in array form. # noqa: E501
+
+    :param component_label: The label of a component in a schema
+    :type component_label: str
+    :param schema_url: The URL of a schema in jsonld or csv form
+    :type schema_url: str
+    :param display_label_type: The type of label to display
+    :type display_label_type: str
+
+    :rtype: Union[ComponentRequirementArray, Tuple[ComponentRequirementArray, int], Tuple[ComponentRequirementArray, int, Dict[str, str]]
+    """
+    return schema_controller_impl.get_component_requirements_array(
+        component_label, schema_url, display_label_type
+    )
+
+
+def get_component_requirements_graph(
+    component_label, schema_url, display_label_type=None
+):  # noqa: E501
+    """Given a source model component (see https://w3id.org/biolink/vocab/category for definnition of component), return all components required by it in graph form.
+
+    Given a source model component (see https://w3id.org/biolink/vocab/category for definnition of component), return all components required by it in graph form. # noqa: E501
+
+    :param component_label: The label of a component in a schema
+    :type component_label: str
+    :param schema_url: The URL of a schema in jsonld or csv form
+    :type schema_url: str
+    :param display_label_type: The type of label to display
+    :type display_label_type: str
+
+    :rtype: Union[ComponentRequirementGraph, Tuple[ComponentRequirementGraph, int], Tuple[ComponentRequirementGraph, int, Dict[str, str]]
+    """
+    return schema_controller_impl.get_component_requirements_graph(
+        component_label, schema_url, display_label_type
+    )
+
+
 def get_connected_node_pair_array(
     schema_url, relationship_type, display_label_type=None
 ):  # noqa: E501

apps/schematic/api/schematic_api/controllers/schema_controller_impl.py

@@ -9,8 +9,12 @@
 from schematic.visualization.attributes_explorer import AttributesExplorer  # type: ignore
 from schematic.utils.schema_utils import get_property_label_from_display_name  # type: ignore
 from schematic.utils.schema_utils import DisplayLabelType  # type: ignore
+from schematic.models.metadata import MetadataModel  # type: ignore
 
 from schematic_api.models.basic_error import BasicError
+from schematic_api.models.component_requirement_subgraph import (
+    ComponentRequirementSubgraph,
+)
 from schematic_api.models.node_property_array import NodePropertyArray
 from schematic_api.models.validation_rule import ValidationRule
 from schematic_api.models.validation_rule_array import ValidationRuleArray
@@ -62,6 +66,72 @@ def get_component(
     return result, status
 
 
+@handle_exceptions
+def get_component_requirements_array(
+    component_label: str,
+    schema_url: str,
+    display_label_type: DisplayLabelType,
+) -> tuple[Union[list[str], BasicError], int]:
+    """Gets the input components required components
+
+    Args:
+        component_label (str): The label of the component
+        schema_url (str): The URL of the schema in json form
+        display_label_type (DisplayLabelType):
+           The type of label to use as display
+           Defaults to "class_label"
+    Returns:
+        tuple[Union[ComponentRequirementArray, BasicError], int]: A tuple
+          item 1 is either the required coponents or an error
+          item 2 is the status
+    """
+    schema_path = download_schema_file_as_jsonld(schema_url)
+    metadata_model = MetadataModel(
+        inputMModelLocation=schema_path,
+        inputMModelLocationType="local",
+        data_model_labels=display_label_type,
+    )
+    result = metadata_model.get_component_requirements(
+        source_component=component_label, as_graph=False
+    )
+    status = 200
+    return result, status
+
+
+@handle_exceptions
+def get_component_requirements_graph(
+    component_label: str,
+    schema_url: str,
+    display_label_type: DisplayLabelType,
+) -> tuple[Union[list[ComponentRequirementSubgraph], BasicError], int]:
+    """Gets the input components required components
+
+    Args:
+        component_label (str): The label of the component
+        schema_url (str): The URL of the schema in json form
+        display_label_type (DisplayLabelType):
+           The type of label to use as display
+           Defaults to "class_label"
+    Returns:
+        tuple[Union[ComponentRequirementGrpah, BasicError], int]: A tuple
+          item 1 is either the required coponents or an error
+          item 2 is the status
+    """
+    schema_path = download_schema_file_as_jsonld(schema_url)
+    metadata_model = MetadataModel(
+        inputMModelLocation=schema_path,
+        inputMModelLocationType="local",
+        data_model_labels=display_label_type,
+    )
+    results = metadata_model.get_component_requirements(
+        source_component=component_label, as_graph=True
+    )
+    result = [ComponentRequirementSubgraph(result[0], result[1]) for result in results]
+
+    status = 200
+    return result, status
+
+
 def get_connected_node_pairs_from_schematic(
     relationship_type: str,
     schema_url: str,

apps/schematic/api/schematic_api/models/__init__.py

@@ -5,6 +5,9 @@
 # import models into model package
 from schematic_api.models.asset_type import AssetType
 from schematic_api.models.basic_error import BasicError
+from schematic_api.models.component_requirement_array import ComponentRequirementArray
+from schematic_api.models.component_requirement_graph import ComponentRequirementGraph
+from schematic_api.models.component_requirement_subgraph import ComponentRequirementSubgraph
 from schematic_api.models.connected_node_pair import ConnectedNodePair
 from schematic_api.models.connected_node_pair_array import ConnectedNodePairArray
 from schematic_api.models.connected_node_pair_page import ConnectedNodePairPage

apps/schematic/api/schematic_api/models/component_requirement_array.py

@@ -0,0 +1,64 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from datetime import date, datetime  # noqa: F401
+
+from typing import List, Dict  # noqa: F401
+
+from schematic_api.models.base_model_ import Model
+from schematic_api import util
+
+
+class ComponentRequirementArray(Model):
+    """NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+
+    Do not edit the class manually.
+    """
+
+    def __init__(self, component_requirements_list=None):  # noqa: E501
+        """ComponentRequirementArray - a model defined in OpenAPI
+
+        :param component_requirements_list: The component_requirements_list of this ComponentRequirementArray.  # noqa: E501
+        :type component_requirements_list: List[str]
+        """
+        self.openapi_types = {
+            'component_requirements_list': List[str]
+        }
+
+        self.attribute_map = {
+            'component_requirements_list': 'componentRequirementsList'
+        }
+
+        self._component_requirements_list = component_requirements_list
+
+    @classmethod
+    def from_dict(cls, dikt) -> 'ComponentRequirementArray':
+        """Returns the dict as a model
+
+        :param dikt: A dict.
+        :type: dict
+        :return: The ComponentRequirementArray of this ComponentRequirementArray.  # noqa: E501
+        :rtype: ComponentRequirementArray
+        """
+        return util.deserialize_model(dikt, cls)
+
+    @property
+    def component_requirements_list(self):
+        """Gets the component_requirements_list of this ComponentRequirementArray.
+
+
+        :return: The component_requirements_list of this ComponentRequirementArray.
+        :rtype: List[str]
+        """
+        return self._component_requirements_list
+
+    @component_requirements_list.setter
+    def component_requirements_list(self, component_requirements_list):
+        """Sets the component_requirements_list of this ComponentRequirementArray.
+
+
+        :param component_requirements_list: The component_requirements_list of this ComponentRequirementArray.
+        :type component_requirements_list: List[str]
+        """
+
+        self._component_requirements_list = component_requirements_list