Merge branch 'develop' into develop-table-replace

Author: GiaJordan

api/openapi/api.yaml

@@ -528,9 +528,17 @@ paths:
           description: ID of view listing all project data assets. For example, for Synapse this would be the Synapse ID of the fileview listing all data assets for a given project.(i.e. master_fileview in config.yml)
           example: syn23643253
           required: true
+        - in: query
+          name: return_type
+          schema:
+            type: string
+            enum: ["json", "csv"]
+          description: Type of return
+          example: 'json'
+          required: true
       responses:
         "200":
-          description: A list of json
+          description: csv file path or json
         "500":
           description: Check schematic log. 
       tags:
@@ -677,4 +685,124 @@ paths:
         "500":
           description: Check schematic log. 
       tags:
-        - Schema Operation
+        - Schema Operation
+        
+        
+  /explorer/get_node_dependencies:
+    get:
+      summary: Get the immediate dependencies that are related to a given source node
+      description: Get the immediate dependencies that are related to a given source node
+      operationId: api.routes.get_node_dependencies
+      parameters:
+        - in: query
+          name: schema_url
+          schema:
+            type: string
+          description: Data Model URL
+          example: >-
+            https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld
+          required: true
+        - in: query
+          name: source_node
+          schema:
+            type: string
+            nullable: false
+          description: The node whose dependencies are needed
+          example: Patient
+          required: true
+        - in: query
+          name: return_display_names
+          schema:
+            type: boolean
+            nullable: true
+          description: Return display names or not
+          required: false
+          example: true
+        - in: query
+          name: return_schema_ordered
+          schema:
+            type: boolean
+            nullable: true
+          description: Return schema ordered or not
+          required: false
+          example: true
+      responses:
+        "200":
+          description: List of nodes that are dependent on the source node.
+        "500":
+          description: Check schematic log.
+      tags:
+        - Schema Operation
+        
+  /explorer/get_property_label_from_display_name:
+    get:
+      summary: Converts a given display name string into a proper property label string
+      description: Converts a given display name string into a proper property label string
+      operationId: api.routes.get_property_label_from_display_name
+      parameters:
+        - in: query
+          name: schema_url
+          schema:
+            type: string
+          description: Data Model URL
+          example: >-
+            https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld
+          required: true
+        - in: query
+          name: display_name
+          schema:
+            type: string
+            nullable: false
+          description: The display name to be converted
+          example: MolecularEntity
+          required: true
+        - in: query
+          name: strict_camel_case
+          schema:
+            type: boolean
+            nullable: false
+          description: If true the more strict way of
+            converting to camel case is used.
+      responses:
+        "200":
+          description: The property label of the display name.
+        "500":
+          description: Check schematic log. 
+      tags:
+        - Schema Operation
+      
+  /explorer/get_node_range:
+    get:
+      summary: Get all the valid values that are associated with a node label.
+      description: Get all the valid values that are associated with a node label.
+      operationId: api.routes.get_node_range
+      parameters:
+        - in: query
+          name: schema_url
+          schema:
+            type: string
+          description: Data Model URL
+          example: >-
+            https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld
+          required: true
+        - in: query
+          name: node_label
+          schema:
+            type: string
+            nullable: false
+          description: Node / term for which you need to retrieve the range.
+          example: FamilyHistory
+          required: true
+        - in: query
+          name: return_display_names
+          schema:
+            type: boolean
+          description: If true returns the display names of the nodes.
+          required: false
+      responses:
+        "200":
+          description: A list of nodes.
+        "500":
+          description: Check schematic log.
+      tags:
+        - Schema Operation

api/routes.py

@@ -1,3 +1,4 @@
+from email import generator
 import os
 import shutil
 import tempfile
@@ -293,7 +294,7 @@ def download_manifest(input_token, dataset_id, asset_view, as_json, new_manifest
 
     return manifest_local_file_path
 
-def get_asset_view_table(input_token, asset_view):
+def get_asset_view_table(input_token, asset_view, return_type):
     # call config handler
     config_handler(asset_view=asset_view)
 
@@ -303,12 +304,15 @@ def get_asset_view_table(input_token, asset_view):
     # get file view table
     file_view_table_df = store.getStorageFileviewTable()
 
-    # convert pandas dataframe to csv
-    path = os.getcwd()
-    export_path = os.path.join(path, 'tests/data/file_view_table.csv')
-    file_view_table_df.to_csv(export_path, index=False)
-
-    return export_path
+    # return different results based on parameter
+    if return_type == "json":
+        json_res = file_view_table_df.to_json()
+        return json_res
+    else:
+        path = os.getcwd()
+        export_path = os.path.join(path, 'tests/data/file_view_table.csv')
+        file_view_table_df.to_csv(export_path, index=False)
+        return export_path
 
 
 def get_project_manifests(input_token, project_id, asset_view):
@@ -385,4 +389,77 @@ def find_class_specific_properties(schema_url, schema_class):
     # return properties
     properties = se.find_class_specific_properties(schema_class)
 
-    return properties
+    return properties
+
+
+def get_node_dependencies(
+    schema_url: str,
+    source_node: str,
+    return_display_names: bool = True,
+    return_schema_ordered: bool = True
+) -> list[str]:
+    """Get the immediate dependencies that are related to a given source node.
+
+    Args:
+        schema_url (str): Data Model URL
+        source_node (str): The node whose dependencies are needed.
+        return_display_names (bool, optional):
+            If True, return list of display names of each of the dependencies.
+            If False, return list of node labels of each of the dependencies.
+            Defaults to True.
+        return_schema_ordered (bool, optional):
+            If True, return the dependencies of the node following the order of the schema (slower).
+            If False, return dependencies from graph without guaranteeing schema order (faster).
+            Defaults to True.
+
+    Returns:
+        list[str]: List of nodes that are dependent on the source node.
+    """
+    gen = SchemaGenerator(path_to_json_ld=schema_url)
+    dependencies = gen.get_node_dependencies(
+        source_node, return_display_names, return_schema_ordered
+    )
+    return dependencies
+
+
+def get_property_label_from_display_name(
+    schema_url: str,
+    display_name: str,
+    strict_camel_case: bool = False
+) -> str:
+    """Converts a given display name string into a proper property label string
+
+    Args:
+        schema_url (str): Data Model URL
+        display_name (str): The display name to be converted
+        strict_camel_case (bool, optional): If true the more strict way of
+            converting to camel case is used.
+
+    Returns:
+        str: The property label of the display name
+    """
+    explorer = SchemaExplorer()
+    explorer.load_schema(schema_url)
+    label = explorer.get_property_label_from_display_name(display_name, strict_camel_case)
+    return label
+
+
+def get_node_range(
+    schema_url: str,
+    node_label: str,
+    return_display_names: bool = True
+) -> list[str]:
+    """Get the range, i.e., all the valid values that are associated with a node label.
+
+    Args:
+        schema_url (str): Data Model URL
+        node_label (str): Node / term for which you need to retrieve the range.
+        return_display_names (bool, optional): If true returns the display names of the nodes.
+            Defaults to True.
+
+    Returns:
+        list[str]: A list of nodes
+    """
+    gen = SchemaGenerator(path_to_json_ld=schema_url)
+    node_range = gen.get_node_range(node_label, return_display_names)
+    return node_range