Add Functional Type to Tool Dependencies

package.json

@@ -1,7 +1,7 @@
 {
     "devDependencies": {
         "@openapitools/openapi-generator-cli": "2.4.13",
-        "release-it": "^14.10.0"
+        "release-it": "^15.0.0"
     },
     "scripts": {
         "generate:server": "openapi-generator-cli generate -g python-flask -o server -i $npm_config_spec",

server/.openapi-generator/VERSION

@@ -1 +1 @@
-5.2.0
+5.4.0

server/openapi_server/controllers/deidentified_note_controller.py

@@ -1,22 +1,18 @@
 import connexion
-from nlpsandbox.model.note_id import NoteId
-from nlpsandbox.model.patient_id import PatientId
+import six
 
 from openapi_server.models.deidentify_request import DeidentifyRequest  # noqa: E501
-from openapi_server.models import DeidentificationStep, DeidentifyResponse, \
-    AnnotationSet, Note
-from openapi_server.phi_deidentifier.deidentifiers import apply_masking_char, \
-    apply_redaction, apply_annotation_type
-from openapi_server.config import Config
-from nlpsandboxclient import client
+from openapi_server.models.deidentify_response import DeidentifyResponse  # noqa: E501
+from openapi_server.models.error import Error  # noqa: E501
+from openapi_server import util
 
 
 def create_deidentified_notes(deidentify_request=None):  # noqa: E501
     """Deidentify a clinical note
 
     Returns the deidentified note # noqa: E501
 
-    :param deidentify_request:
+    :param deidentify_request: 
     :type deidentify_request: dict | bytes
 
     :rtype: DeidentifyResponse

server/openapi_server/controllers/tool_controller.py

@@ -1,8 +1,10 @@
+from typing import List
+
 from nlpsandboxclient import client
 
 from openapi_server.models.tool import Tool  # noqa: E501
 from ..config import Config
-from ..models import License, ToolDependencies, ToolType
+from ..models import License, ToolDependencies, ToolType, ToolDependency
 
 
 def get_tool():  # noqa: E501
@@ -37,17 +39,21 @@ def get_tool_dependencies():  # noqa: E501
     :rtype: ToolDependencies
     """
     config = Config()
-    tool_dependencies = []
-    for hostname in (
-            config.date_annotator_api_url,
-            config.person_name_annotator_api_url,
-            config.location_annotator_api_url,
-            config.contact_annotator_api_url,
-            config.id_annotator_api_url,
+    tool_dependencies: List[ToolDependency] = []
+    for functional_type, hostname in (
+            (ToolType.DATE_ANNOTATOR, config.date_annotator_api_url),
+            (ToolType.PERSON_NAME_ANNOTATOR,
+             config.person_name_annotator_api_url),
+            (ToolType.LOCATION_ANNOTATOR, config.location_annotator_api_url),
+            (ToolType.CONTACT_ANNOTATOR, config.contact_annotator_api_url),
+            (ToolType.ID_ANNOTATOR, config.id_annotator_api_url),
     ):
         client_tool = client.get_tool(host=hostname)
         tool = Tool.from_dict({client_tool.attribute_map[key]: value
                                for key, value in
                                client_tool.to_dict().items()})
-        tool_dependencies.append(tool)
-    return ToolDependencies(tools=tool_dependencies)
+        tool_dependency = ToolDependency(
+            tool=tool, functional_type=functional_type)
+        tool_dependencies.append(tool_dependency)
+        print('ASDFEHASWEJ')
+    return ToolDependencies(tool_dependencies=tool_dependencies)

server/openapi_server/models/__init__.py

@@ -13,6 +13,7 @@
 from openapi_server.models.license import License
 from openapi_server.models.masking_char_config import MaskingCharConfig
 from openapi_server.models.note import Note
+from openapi_server.models.programming_language import ProgrammingLanguage
 from openapi_server.models.text_annotation import TextAnnotation
 from openapi_server.models.text_contact_annotation import TextContactAnnotation
 from openapi_server.models.text_contact_annotation_all_of import TextContactAnnotationAllOf
@@ -25,4 +26,5 @@
 from openapi_server.models.text_person_name_annotation import TextPersonNameAnnotation
 from openapi_server.models.tool import Tool
 from openapi_server.models.tool_dependencies import ToolDependencies
+from openapi_server.models.tool_dependency import ToolDependency
 from openapi_server.models.tool_type import ToolType

server/openapi_server/models/programming_language.py

@@ -0,0 +1,95 @@
+# coding: utf-8
+
+from __future__ import absolute_import
+from datetime import date, datetime  # noqa: F401
+
+from typing import List, Dict  # noqa: F401
+
+from openapi_server.models.base_model_ import Model
+from openapi_server import util
+
+
+class ProgrammingLanguage(Model):
+    """NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+
+    Do not edit the class manually.
+    """
+
+    """
+    allowed enum values
+    """
+    APL = "APL"
+    ASP = "ASP"
+    ADA = "Ada"
+    ASSEMBLY = "Assembly"
+    AWK = "Awk"
+    BASIC = "Basic"
+    C = "C"
+    C_ = "C#"
+    C_ = "C++"
+    CLOJURE = "Clojure"
+    CYTHON = "Cython"
+    DART = "Dart"
+    DELPHI_KYLIX = "Delphi/Kylix"
+    EMACS_LISP = "Emacs-Lisp"
+    ERLANG = "Erlang"
+    EULER = "Euler"
+    FORTH = "Forth"
+    FORTRAN = "Fortran"
+    GO = "Go"
+    GROOVY = "Groovy"
+    HASKELL = "Haskell"
+    JAVA = "Java"
+    JAVASCRIPT = "JavaScript"
+    JULIA = "Julia"
+    KOTLIN = "Kotlin"
+    LISP = "Lisp"
+    LOGO = "Logo"
+    MATLAB = "MATLAB"
+    ML = "ML"
+    OCAML = "OCaml"
+    OBJECT_PASCAL = "Object Pascal"
+    OBJECTIVE_C = "Objective C"
+    OTHER = "Other"
+    OTHER_SCRIPTING_ENGINES = "Other Scripting Engines"
+    PHP = "PHP"
+    PL_SQL = "PL/SQL"
+    PASCAL = "Pascal"
+    PERL = "Perl"
+    PIKE = "Pike"
+    PROLOG = "Prolog"
+    PYTHON = "Python"
+    R = "R"
+    REBOL = "REBOL"
+    REXX = "Rexx"
+    RUBY = "Ruby"
+    RUST = "Rust"
+    SCALA = "Scala"
+    SCHEME = "Scheme"
+    SQL = "SQL"
+    TCL = "Tcl"
+    TYPESCRIPT = "TypeScript"
+    UNIX_SHELL = "Unix Shell"
+    VISUAL_BASIC = "Visual Basic"
+    YACC = "YACC"
+    ZOPE = "Zope"
+    def __init__(self):  # noqa: E501
+        """ProgrammingLanguage - a model defined in OpenAPI
+
+        """
+        self.openapi_types = {
+        }
+
+        self.attribute_map = {
+        }
+
+    @classmethod
+    def from_dict(cls, dikt) -> 'ProgrammingLanguage':
+        """Returns the dict as a model
+
+        :param dikt: A dict.
+        :type: dict
+        :return: The ProgrammingLanguage of this ProgrammingLanguage.  # noqa: E501
+        :rtype: ProgrammingLanguage
+        """
+        return util.deserialize_model(dikt, cls)

server/openapi_server/models/tool.py

@@ -7,11 +7,13 @@
 
 from openapi_server.models.base_model_ import Model
 from openapi_server.models.license import License
+from openapi_server.models.programming_language import ProgrammingLanguage
 from openapi_server.models.tool_type import ToolType
 import re
 from openapi_server import util
 
 from openapi_server.models.license import License  # noqa: E501
+from openapi_server.models.programming_language import ProgrammingLanguage  # noqa: E501
 from openapi_server.models.tool_type import ToolType  # noqa: E501
 import re  # noqa: E501
 
@@ -21,7 +23,7 @@ class Tool(Model):
     Do not edit the class manually.
     """
 
-    def __init__(self, name=None, version=None, license=None, repository=None, description=None, author=None, author_email=None, url=None, type=None, api_version=None):  # noqa: E501
+    def __init__(self, name=None, version=None, license=None, repository=None, description=None, author=None, author_email=None, url=None, type=None, api_version=None, programming_languages=None):  # noqa: E501
         """Tool - a model defined in OpenAPI
 
         :param name: The name of this Tool.  # noqa: E501
@@ -44,6 +46,8 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
         :type type: ToolType
         :param api_version: The api_version of this Tool.  # noqa: E501
         :type api_version: str
+        :param programming_languages: The programming_languages of this Tool.  # noqa: E501
+        :type programming_languages: list[ProgrammingLanguage]
         """
         self.openapi_types = {
             'name': str,
@@ -55,7 +59,8 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
             'author_email': str,
             'url': str,
             'type': ToolType,
-            'api_version': str
+            'api_version': str,
+            'programming_languages': list[ProgrammingLanguage]
         }
 
         self.attribute_map = {
@@ -68,7 +73,8 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
             'author_email': 'authorEmail',
             'url': 'url',
             'type': 'type',
-            'api_version': 'apiVersion'
+            'api_version': 'apiVersion',
+            'programming_languages': 'programmingLanguages'
         }
 
         self._name = name
@@ -81,6 +87,7 @@ def __init__(self, name=None, version=None, license=None, repository=None, descr
         self._url = url
         self._type = type
         self._api_version = api_version
+        self._programming_languages = programming_languages
 
     @classmethod
     def from_dict(cls, dikt) -> 'Tool':
@@ -354,3 +361,28 @@ def api_version(self, api_version):
             raise ValueError("Invalid value for `api_version`, must be a follow pattern or equal to `/^(0|[1-9]\d*)\.(0|[1-9]\d*)\.(0|[1-9]\d*)(?:-((?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\+([0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$/`")  # noqa: E501
 
         self._api_version = api_version
+
+    @property
+    def programming_languages(self):
+        """Gets the programming_languages of this Tool.
+
+        The programming languages used to develop this tool  # noqa: E501
+
+        :return: The programming_languages of this Tool.
+        :rtype: list[ProgrammingLanguage]
+        """
+        return self._programming_languages
+
+    @programming_languages.setter
+    def programming_languages(self, programming_languages):
+        """Sets the programming_languages of this Tool.
+
+        The programming languages used to develop this tool  # noqa: E501
+
+        :param programming_languages: The programming_languages of this Tool.
+        :type programming_languages: list[ProgrammingLanguage]
+        """
+        if programming_languages is not None and len(programming_languages) < 0:
+            raise ValueError("Invalid value for `programming_languages`, number of items must be greater than or equal to `0`")  # noqa: E501
+
+        self._programming_languages = programming_languages

server/openapi_server/models/tool_dependencies.py

@@ -6,32 +6,32 @@
 from typing import List, Dict  # noqa: F401
 
 from openapi_server.models.base_model_ import Model
-from openapi_server.models.tool import Tool
+from openapi_server.models.tool_dependency import ToolDependency
 from openapi_server import util
 
-from openapi_server.models.tool import Tool  # noqa: E501
+from openapi_server.models.tool_dependency import ToolDependency  # noqa: E501
 
 class ToolDependencies(Model):
     """NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
 
     Do not edit the class manually.
     """
 
-    def __init__(self, tools=None):  # noqa: E501
+    def __init__(self, tool_dependencies=None):  # noqa: E501
         """ToolDependencies - a model defined in OpenAPI
 
-        :param tools: The tools of this ToolDependencies.  # noqa: E501
-        :type tools: List[Tool]
+        :param tool_dependencies: The tool_dependencies of this ToolDependencies.  # noqa: E501
+        :type tool_dependencies: List[ToolDependency]
         """
         self.openapi_types = {
-            'tools': List[Tool]
+            'tool_dependencies': List[ToolDependency]
         }
 
         self.attribute_map = {
-            'tools': 'tools'
+            'tool_dependencies': 'toolDependencies'
         }
 
-        self._tools = tools
+        self._tool_dependencies = tool_dependencies
 
     @classmethod
     def from_dict(cls, dikt) -> 'ToolDependencies':
@@ -45,26 +45,26 @@ def from_dict(cls, dikt) -> 'ToolDependencies':
         return util.deserialize_model(dikt, cls)
 
     @property
-    def tools(self):
-        """Gets the tools of this ToolDependencies.
+    def tool_dependencies(self):
+        """Gets the tool_dependencies of this ToolDependencies.
 
-        A list of tools  # noqa: E501
+        A list of tool dependencies  # noqa: E501
 
-        :return: The tools of this ToolDependencies.
-        :rtype: List[Tool]
+        :return: The tool_dependencies of this ToolDependencies.
+        :rtype: List[ToolDependency]
         """
-        return self._tools
+        return self._tool_dependencies
 
-    @tools.setter
-    def tools(self, tools):
-        """Sets the tools of this ToolDependencies.
+    @tool_dependencies.setter
+    def tool_dependencies(self, tool_dependencies):
+        """Sets the tool_dependencies of this ToolDependencies.
 
-        A list of tools  # noqa: E501
+        A list of tool dependencies  # noqa: E501
 
-        :param tools: The tools of this ToolDependencies.
-        :type tools: List[Tool]
+        :param tool_dependencies: The tool_dependencies of this ToolDependencies.
+        :type tool_dependencies: List[ToolDependency]
         """
-        if tools is None:
-            raise ValueError("Invalid value for `tools`, must not be `None`")  # noqa: E501
+        if tool_dependencies is None:
+            raise ValueError("Invalid value for `tool_dependencies`, must not be `None`")  # noqa: E501
 
-        self._tools = tools
+        self._tool_dependencies = tool_dependencies