Merge branch 'main' into openchallenges/filter-challenges-by-operation

apps/schematic/api/.gitignore

@@ -70,6 +70,8 @@ target/
 #secrets
 *secrets*
 schematic_service_account_creds.json
+private_localhost_certificate.crt
+private_localhost.key
 
 #config files
 config.yaml

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/pyproject.toml

@@ -11,7 +11,7 @@ python = "3.10.14"
 connexion = {version = "2.14.1", extras = ["swagger-ui"]}
 swagger-ui-bundle = "0.0.9"
 python-dateutil = "2.8.2"
-Flask = "2.1.3"
+Flask = "2.2.5"
 Flask-Cors = "3.0.10"
 schematicpy = "24.4.1"
 # jsonschema isn't a direct import, but is used by connexion.

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

@@ -11,6 +11,9 @@
 from schematic.utils.schema_utils import DisplayLabelType  # 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
@@ -27,6 +30,29 @@
 from schematic_api.controllers.paging import Page
 
 
+def create_data_model_graph_explorer(
+    schema_url: str, display_label_type: DisplayLabelType
+) -> DataModelGraphExplorer:
+    """Creates a DataModelGraphExplorer for use in variopus endpoints
+
+    Args:
+        schema_url (str): The URL of the schema in json form
+        display_label_type (DisplayLabelType):
+           The type of label to use as display
+
+    Returns:
+        DataModelGraphExplorer: _description_
+    """
+    data_model_parser = DataModelParser(path_to_data_model=schema_url)
+    parsed_data_model = data_model_parser.parse_model()
+    data_model_grapher = DataModelGraph(
+        attribute_relationships_dict=parsed_data_model,
+        data_model_labels=display_label_type,
+    )
+    graph_data_model = data_model_grapher.generate_data_model_graph()
+    return DataModelGraphExplorer(graph_data_model)
+
+
 @handle_exceptions
 def get_component(
     component_label: str,
@@ -66,6 +92,56 @@ 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
+    Returns:
+        tuple[Union[ComponentRequirementArray, BasicError], int]: A tuple
+          item 1 is either the required coponents or an error
+          item 2 is the status
+    """
+    dmge = create_data_model_graph_explorer(schema_url, display_label_type)
+    result = dmge.get_component_requirements(source_component=component_label)
+    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
+    Returns:
+        tuple[Union[ComponentRequirementGrpah, BasicError], int]: A tuple
+          item 1 is either the required coponents or an error
+          item 2 is the status
+    """
+    dmge = create_data_model_graph_explorer(schema_url, display_label_type)
+    graph = dmge.get_component_requirements_graph(source_component=component_label)
+    edges: list[tuple[str, str]] = graph.edges()
+    result = [ComponentRequirementSubgraph(edge[0], edge[1]) for edge in edges]
+    status = 200
+    return result, status
+
+
 def get_connected_node_pairs_from_schematic(
     relationship_type: str,
     schema_url: str,
@@ -83,14 +159,7 @@ def get_connected_node_pairs_from_schematic(
     Returns:
         list[ConnectedNodePair]: A list of connected node pairs
     """
-    data_model_parser = DataModelParser(path_to_data_model=schema_url)
-    parsed_data_model = data_model_parser.parse_model()
-    data_model_grapher = DataModelGraph(
-        attribute_relationships_dict=parsed_data_model,
-        data_model_labels=display_label_type,
-    )
-    graph_data_model = data_model_grapher.generate_data_model_graph()
-    dmge = DataModelGraphExplorer(graph_data_model)
+    dmge = create_data_model_graph_explorer(schema_url, display_label_type)
     relationship_subgraph = dmge.get_subgraph_by_edge_type(relationship_type)
     lst = [list(edge) for edge in relationship_subgraph.edges]
 
@@ -188,14 +257,7 @@ def get_node_is_required_from_schematic(
     Returns:
        bool: Whether or no the node is required
     """
-    data_model_parser = DataModelParser(path_to_data_model=schema_url)
-    parsed_data_model = data_model_parser.parse_model()
-    data_model_grapher = DataModelGraph(
-        attribute_relationships_dict=parsed_data_model,
-        data_model_labels=display_label_type,
-    )
-    graph_data_model = data_model_grapher.generate_data_model_graph()
-    dmge = DataModelGraphExplorer(graph_data_model)
+    dmge = create_data_model_graph_explorer(schema_url, display_label_type)
     return dmge.get_node_required(node_display)
 
 
@@ -294,14 +356,7 @@ def get_node_properties_from_schematic(
     Returns:
         list[str]: A list of properties of the node
     """
-    data_model_parser = DataModelParser(path_to_data_model=schema_url)
-    parsed_data_model = data_model_parser.parse_model()
-    data_model_grapher = DataModelGraph(
-        attribute_relationships_dict=parsed_data_model,
-        data_model_labels=display_label_type,
-    )
-    graph_data_model = data_model_grapher.generate_data_model_graph()
-    dmge = DataModelGraphExplorer(graph_data_model)
+    dmge = create_data_model_graph_explorer(schema_url, display_label_type)
     properties = dmge.find_class_specific_properties(node_label)
     return properties
 
@@ -352,14 +407,7 @@ def get_node_validation_rules_from_schematic(
     Returns:
         list[ValidationRule]: A list of validation_rules of the node
     """
-    data_model_parser = DataModelParser(path_to_data_model=schema_url)
-    parsed_data_model = data_model_parser.parse_model()
-    data_model_grapher = DataModelGraph(
-        attribute_relationships_dict=parsed_data_model,
-        data_model_labels=display_label_type,
-    )
-    graph_data_model = data_model_grapher.generate_data_model_graph()
-    dmge = DataModelGraphExplorer(graph_data_model)
+    dmge = create_data_model_graph_explorer(schema_url, display_label_type)
     rules: list[str] = dmge.get_node_validation_rules(node_display)  # type: ignore
     return [ValidationRule(rule) for rule in rules]
 
@@ -418,14 +466,7 @@ def get_node_dependencies_from_schematic(
         list[Node]: A list of nodes
 
     """
-    data_model_parser = DataModelParser(path_to_data_model=schema_url)
-    parsed_data_model = data_model_parser.parse_model()
-    data_model_grapher = DataModelGraph(
-        attribute_relationships_dict=parsed_data_model,
-        data_model_labels=display_label_type,
-    )
-    graph_data_model = data_model_grapher.generate_data_model_graph()
-    dmge = DataModelGraphExplorer(graph_data_model)
+    dmge = create_data_model_graph_explorer(schema_url, display_label_type)
     nodes = dmge.get_node_dependencies(
         node_label, return_display_names, return_ordered_by_schema
     )