feat(schematic): move visualization operations endpoints (#2252)

* add new endpoints

* added two endpoints

* add new endpoints

* redid exception handling for new endpoints

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

@@ -36,4 +36,5 @@ schematic_api/test/test_storage_controller.py
 schematic_api/test/test_schema_controller.py
 schematic_api/test/test_manifest_validation_controller.py
 schematic_api/test/test_versions_controller.py
+schematic_api/test/test_tangled_tree_controller.py
 tox.ini

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

@@ -5,6 +5,7 @@ schematic_api/controllers/manifest_validation_controller.py
 schematic_api/controllers/schema_controller.py
 schematic_api/controllers/security_controller_.py
 schematic_api/controllers/storage_controller.py
+schematic_api/controllers/tangled_tree_controller.py
 schematic_api/controllers/versions_controller.py
 schematic_api/encoder.py
 schematic_api/models/__init__.py
@@ -39,6 +40,5 @@ schematic_api/models/validation_rules_page.py
 schematic_api/models/validation_rules_page_all_of.py
 schematic_api/openapi/openapi.yaml
 schematic_api/test/__init__.py
-schematic_api/test/test_manifest_validation_controller.py
 schematic_api/typing_utils.py
 schematic_api/util.py

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

@@ -3,8 +3,6 @@
 import os
 import io
 import json
-import urllib.request
-import shutil
 from typing import Union, Any, Optional
 
 import pandas as pd
@@ -13,24 +11,11 @@
 
 from schematic_api.models.manifest_validation_result import ManifestValidationResult
 from schematic_api.models.basic_error import BasicError
-from schematic_api.controllers.utils import handle_exceptions, get_access_token
-
-
-def download_schema_file_as_jsonld(schema_url: str) -> str:
-    """Downloads a schema and saves it as temp file
-
-    Args:
-        schema_url (str): The URL of the schema
-
-    Returns:
-        str: The path fo the schema jsonld file
-    """
-    with urllib.request.urlopen(schema_url) as response:
-        with tempfile.NamedTemporaryFile(
-            delete=False, suffix=".model.jsonld"
-        ) as tmp_file:
-            shutil.copyfileobj(response, tmp_file)
-            return tmp_file.name
+from schematic_api.controllers.utils import (
+    handle_exceptions,
+    get_access_token,
+    download_schema_file_as_jsonld,
+)
 
 
 def save_manifest_json_string_as_csv(manifest_json_string: str) -> str:

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

@@ -13,6 +13,25 @@
 from schematic_api.controllers import schema_controller_impl
 
 
+def get_component(component_label, schema_url, include_index=None):  # noqa: E501
+    """Get all the attributes associated with a specific data model component formatted as a dataframe (stored as a JSON String).
+
+    Get all the attributes associated with a specific data model component formatted as a dataframe (stored as a JSON String). # 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 form
+    :type schema_url: str
+    :param include_index: Whether to include the indexes of the dataframe in the returned JSON string.
+    :type include_index: bool
+
+    :rtype: Union[str, Tuple[str, int], Tuple[str, int, Dict[str, str]]
+    """
+    return schema_controller_impl.get_component(
+        component_label, schema_url, include_index
+    )
+
+
 def get_connected_nodes(schema_url, relationship_type):  # noqa: E501
     """Gets a list of connected node pairs
 
@@ -79,6 +98,19 @@ def get_property_label(
     )
 
 
+def get_schema_attributes(schema_url):  # noqa: E501
+    """Get all the attributes associated with a data model formatted as a dataframe (stored as a JSON String).
+
+    Get all the attributes associated with a data model formatted as a dataframe (stored as a JSON String). # noqa: E501
+
+    :param schema_url: The URL of a schema in jsonld form
+    :type schema_url: str
+
+    :rtype: Union[str, Tuple[str, int], Tuple[str, int, Dict[str, str]]
+    """
+    return schema_controller_impl.get_schema_attributes(schema_url)
+
+
 def list_node_dependencies(
     node_label, schema_url, return_display_names=None, return_ordered_by_schema=None
 ):  # noqa: E501

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

@@ -2,6 +2,7 @@
 from typing import Union, Any
 
 from schematic.schemas.generator import SchemaGenerator, SchemaExplorer  # type: ignore
+from schematic.visualization.attributes_explorer import AttributesExplorer  # type: ignore
 
 from schematic_api.models.basic_error import BasicError
 from schematic_api.models.node_properties_page import NodePropertiesPage
@@ -12,7 +13,37 @@
 from schematic_api.models.node import Node
 from schematic_api.models.connected_nodes_page import ConnectedNodesPage
 from schematic_api.models.connected_nodes import ConnectedNodes
-from schematic_api.controllers.utils import handle_exceptions
+from schematic_api.controllers.utils import (
+    handle_exceptions,
+    download_schema_file_as_jsonld,
+)
+
+
+@handle_exceptions
+def get_component(
+    component_label: str, schema_url: str, include_index: bool = False
+) -> tuple[Union[str, BasicError], int]:
+    """
+    Get all the attributes associated with a specific data model component formatted as a
+    dataframe (stored as a JSON String).
+
+    Args:
+        component_label (str): The label of the component
+        schema_url (str): The URL of the schema in json form
+        include_index (bool): Whether to include the indexes of the dataframe
+
+    Returns:
+        tuple[Union[str, BasicError], int]: A tuple
+          The first item is either the component or an error object
+          The second item is the response status
+    """
+    schema_path = download_schema_file_as_jsonld(schema_url)
+    explorer = AttributesExplorer(schema_path)
+    result: Union[str, BasicError] = explorer.parse_component_attributes(
+        component=component_label, save_file=False, include_index=include_index
+    )
+    status = 200
+    return result, status
 
 
 def get_connected_nodes_from_schematic(
@@ -162,6 +193,27 @@ def get_property_label(
     return result, status
 
 
+@handle_exceptions
+def get_schema_attributes(schema_url: str) -> tuple[Union[str, BasicError], int]:
+    """
+    Get all the attributes associated with a data model formatted as a dataframe
+    (stored as a JSON String).
+
+    Args:
+        schema_url (str): The URL of the schema in json form
+
+    Returns:
+        tuple[Union[str, BasicError], int]: A tuple
+          The first item is either the sttraibutes or an error object
+          The second item is the response status
+    """
+    schema_path = download_schema_file_as_jsonld(schema_url)
+    explorer = AttributesExplorer(schema_path)
+    result: Union[str, BasicError] = explorer.parse_attributes(save_file=False)
+    status = 200
+    return result, status
+
+
 def get_node_properties_from_schematic(
     node_label: str,
     schema_url: str,

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

@@ -0,0 +1,43 @@
+import connexion
+import six
+from typing import Dict
+from typing import Tuple
+from typing import Union
+
+from schematic_api.models.basic_error import BasicError  # noqa: E501
+from schematic_api import util
+from schematic_api.controllers import tangled_tree_controller_impl
+
+
+def get_tangled_tree_layers(schema_url, figure_type=None):  # noqa: E501
+    """Get tangled tree node layers to display for a given data model and figure type
+
+    Get tangled tree node layers to display for a given data model and figure type # noqa: E501
+
+    :param schema_url: The URL of a schema in jsonld form
+    :type schema_url: str
+    :param figure_type: Figure type to generate.
+    :type figure_type: str
+
+    :rtype: Union[str, Tuple[str, int], Tuple[str, int, Dict[str, str]]
+    """
+    return tangled_tree_controller_impl.get_tangled_tree_layers(schema_url, figure_type)
+
+
+def get_tangled_tree_text(schema_url, figure_type=None, text_format=None):  # noqa: E501
+    """Get tangled tree plain or higlighted text to display for a given data model, text formatting and figure type
+
+    Get tangled tree plain or higlighted text to display for a given data model, text formatting and figure type # noqa: E501
+
+    :param schema_url: The URL of a schema in jsonld form
+    :type schema_url: str
+    :param figure_type: Figure type to generate.
+    :type figure_type: str
+    :param text_format: Text formatting type.
+    :type text_format: str
+
+    :rtype: Union[object, Tuple[object, int], Tuple[object, int, Dict[str, str]]
+    """
+    return tangled_tree_controller_impl.get_tangled_tree_text(
+        schema_url, figure_type, text_format
+    )

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

@@ -0,0 +1,71 @@
+"""Tangled tree controllers"""
+
+from typing import Literal, Union
+
+from schematic.visualization.tangled_tree import TangledTree  # type: ignore
+
+from schematic_api.models.basic_error import BasicError
+from schematic_api.controllers.utils import (
+    handle_exceptions,
+    download_schema_file_as_jsonld,
+)
+
+
+@handle_exceptions
+def get_tangled_tree_layers(
+    schema_url: str, figure_type: Literal["component", "dependency"] = "component"
+) -> tuple[Union[str, BasicError], int]:
+    """Gets layers for a tangled tree visualization.
+
+    Args:
+        schema_url (str): The URL to the schema file
+        figure_type (Literal["component", "dependency"]): Figure type to generate.
+
+    Returns:
+        tuple[Union[str, BasicError], int]: A tuple
+          The first item is either the layers or an error object
+          The second item is the response status
+    """
+    schema_path = download_schema_file_as_jsonld(schema_url)
+    tangled_tree = TangledTree(schema_path, figure_type)
+    # Currently TangledTree.get_tangled_tree_layers() returns either an empty list if
+    # save_file=False or a list of one string if save_file=False.
+    # The API should output just the string.
+    # TangledTree.get_tangled_tree_layers() will likely get changed in the future to return
+    # just a string.
+    layers_list: list[str] = tangled_tree.get_tangled_tree_layers(save_file=False)
+    if len(layers_list) == 0:
+        raise ValueError("TangledTree.get_tangled_tree_layers() returned an empty list")
+    result: Union[str, BasicError] = layers_list[0]
+    status = 200
+
+    return result, status
+
+
+@handle_exceptions
+def get_tangled_tree_text(
+    schema_url: str,
+    figure_type: Literal["component", "dependency"] = "component",
+    text_format: Literal["plain", "highlighted"] = "plain",
+) -> tuple[Union[str, BasicError], int]:
+    """Gets text for a tangled tree visualization.
+
+    Args:
+        schema_url (str): The URL to the schema file
+        figure_type (Literal["component", "dependency"]): Figure type to generate.
+        text_format (Literal["plain", "highlighted"]):  Determines the type of text
+          rendering to return
+
+      Returns:
+        tuple[Union[str, BasicError], int]: A tuple
+          The first item is either the text or an error object
+          The second item is the response status
+    """
+    schema_path = download_schema_file_as_jsonld(schema_url)
+    tangled_tree = TangledTree(schema_path, figure_type)
+    result: Union[str, BasicError] = tangled_tree.get_text_for_tangled_tree(
+        text_format, save_file=False
+    )
+    status = 200
+
+    return result, status

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

@@ -1,4 +1,7 @@
 from typing import Callable, Union, Any, Optional
+import urllib.request
+import shutil
+import tempfile
 
 from flask import request  # type: ignore
 from synapseclient.core.exceptions import (  # type: ignore
@@ -61,3 +64,20 @@ def func(*args: Any, **kwargs: Any) -> tuple[Union[Any, BasicError], int]:
             return res, status
 
     return func
+
+
+def download_schema_file_as_jsonld(schema_url: str) -> str:
+    """Downloads a schema and saves it as temp file
+
+    Args:
+        schema_url (str): The URL of the schema
+
+    Returns:
+        str: The path fo the schema jsonld file
+    """
+    with urllib.request.urlopen(schema_url) as response:
+        with tempfile.NamedTemporaryFile(
+            delete=False, suffix=".model.jsonld"
+        ) as tmp_file:
+            shutil.copyfileobj(response, tmp_file)
+            return tmp_file.name