feat: add support for external ontologies (dev-512) (#170)

* update documentation

* add more external ontologies

* code cleanup

* add test data

* clean up code

* update author information

* update bazel version

* rename variables in get method

* make group optional for dsp-tools get

* allow IRIs to not be reduced

* fix merge conflict

* code changes after review

* Update docstring for createDefinitionFileObj

docs/dsp-tools-create-ontologies.md

@@ -891,19 +891,19 @@ Example for a resource definition:
 
 ## Referencing Ontologies
 
-For several fields, such as `super` in both `resources` and `properties` or `propname` in `cardinalities`,
-it is necessary to reference entities that are defined elsewhere. The following cases are possible.
+For several fields, such as `super` in both `resources` and `properties` or `propname` in `cardinalities`
+it is necessary to reference entities that are defined elsewhere. The following cases are possible:
 
-- DSP-API internals: These must be written *without* leading colon and should not be a fully qualified IRI.  
+- DSP API internals: They are referenced as such and do not have a leading colon.  
   E.g. `Resource`, `DocumentRepresentation` or `hasValue`
-- An external ontology: The ontology must be defined in the [prefixes](dsp-tools-create.md#prefixes-object)
-  This prefix should be used for referencing the ontology.  
+- An external ontology: The ontology must be defined in the [prefixes](dsp-tools-create.md#prefixes-object) section.
+  The prefix can then be used for referencing the ontology.  
   E.g. `foaf:familyName` or `sdo:Organization`
 - The current ontology: Within an ontology definition, references can be made by prepending a colon without a prefix.  
-  E.g. `:hasName`  
-  Optionally, an explicit prefix can be used, in this case the ontology must be added to the
-  [prefixes](dsp-tools-create.md#prefixes-object) and the prefix must be identical to the ontology's `name`.  
+  E.g. `:hasName`
+  Optionally, an explicit prefix can be used. In this case the ontology must be added to the
+  [prefixes](dsp-tools-create.md#prefixes-object) section and the prefix must be identical to the ontology's `name`.  
 - A different ontology defined in the same file: Within one data model file, multiple ontologies can be defined.
   These will be created in the exact order they appear in the `ontologies` array. Once an ontology has been created,
-  it can be referenced by the following ontologies via its name: `first-onto:hasName`. It is not necessary to add 
+  it can be referenced by the following ontologies by its name, e.g. `first-onto:hasName`. It is not necessary to add 
   `first-onto` to the prefixes.

docs/dsp-tools-create.md

@@ -52,10 +52,10 @@ A complete data model definition for DSP looks like this:
 
 `"prefixes": { "prefix": "<iri>", ...}`
 
-The `prefixes` object contains the prefixes of external ontologies that are used in the current project. All prefixes
-are composed of the actual prefix and an IRI. The prefix is used as an abbreviation so one does not have to write the
-full qualified IRI each time it is used. So, instead of writing a property called "familyname" as
-`http://xmlns.com/foaf/0.1/familyName` one can simply use `foaf:familyName`.
+The `prefixes` object contains the prefixes of external ontologies that are used in the current file. All prefixes
+are composed of the prefix and a URI. The prefix is used as namespace so one does not have to write the
+fully qualified name of the referenced object each time it is used. Instead of writing a property called "familyName" 
+as `http://xmlns.com/foaf/0.1/familyName` one can simply write `foaf:familyName`.
 
 ```json
 {
@@ -66,8 +66,9 @@ full qualified IRI each time it is used. So, instead of writing a property calle
 }
 ```
 
-It is not necessary to define prefixes for the ontologies that are defined in this file. Ontologies in the same
-file can refer to each other via their name. See also [here](./dsp-tools-create-ontologies.md#referencing-ontologies).
+It is not necessary to define prefixes for the ontologies that are defined in the same file. Ontologies in the same
+file can be referenced by their name. See [this section](./dsp-tools-create-ontologies.md#referencing-ontologies) for
+more information about referencing ontologies.
 
 ### "$schema" object
 

knora/dsplib/models/connection.py

@@ -1,6 +1,6 @@
 import json
 import re
-from typing import Optional, Union
+from typing import Optional, Union, Any
 
 import requests
 from pystrict import strict
@@ -159,7 +159,7 @@ def post(self, path: str, jsondata: Optional[str] = None):
         result = req.json()
         return result
 
-    def get(self, path: str, headers: Optional[dict[str, str]] = None):
+    def get(self, path: str, headers: Optional[dict[str, str]] = None) -> dict[str, Any]:
         """
         Get data from a server using a HTTP GET request
         :param path: Path of RESTful route
@@ -169,22 +169,21 @@ def get(self, path: str, headers: Optional[dict[str, str]] = None):
 
         if path[0] != '/':
             path = '/' + path
-        if self._token is None:
-            if headers is None:
-                req = requests.get(self._server + path)
+        if not self._token:
+            if not headers:
+                response = requests.get(self._server + path)
             else:
-                req = requests.get(self._server + path, headers)
+                response = requests.get(self._server + path, headers)
         else:
-            if headers is None:
-                req = requests.get(self._server + path,
-                                   headers={'Authorization': 'Bearer ' + self._token})
+            if not headers:
+                response = requests.get(self._server + path, headers={'Authorization': 'Bearer ' + self._token})
             else:
                 headers['Authorization'] = 'Bearer ' + self._token
-                req = requests.get(self._server + path, headers)
+                response = requests.get(self._server + path, headers)
 
-        self.on_api_error(req)
-        result = req.json()
-        return result
+        self.on_api_error(response)
+        json_response = response.json()
+        return json_response
 
     def put(self, path: str, jsondata: Optional[str] = None, content_type: str = 'application/json'):
         """

knora/dsplib/models/group.py

@@ -160,8 +160,8 @@ def has_changed(self) -> bool:
 
     @classmethod
     def fromJsonObj(cls, con: Connection, json_obj: Any):
-        id = json_obj.get('id')
-        if id is None:
+        group_id = json_obj.get('id')
+        if group_id is None:
             raise BaseError('Group "id" is missing')
         name = json_obj.get('name')
         if name is None:
@@ -181,7 +181,7 @@ def fromJsonObj(cls, con: Connection, json_obj: Any):
             raise BaseError("Status is missing")
         return cls(con=con,
                    name=name,
-                   id=id,
+                   id=group_id,
                    descriptions=descriptions,
                    project=project,
                    selfjoin=selfjoin,
@@ -249,16 +249,14 @@ def getAllGroups(con: Connection) -> Optional[list[Group]]:
             return None
 
     @staticmethod
-    def getAllGroupsForProject(con: Connection, proj_shortcode: str) -> list[Group]:
-        result = con.get(Group.ROUTE)
-        if 'groups' not in result:
-            raise BaseError("Request got no groups!")
-        all_groups = result["groups"]
-        project_groups = []
-        for group in all_groups:
-            if group["project"]["id"] == "http://rdfh.ch/projects/" + proj_shortcode:
-                project_groups.append(group)
-        return list(map(lambda a: Group.fromJsonObj(con, a), project_groups))
+    def getAllGroupsForProject(con: Connection, proj_shortcode: str) -> Optional[list[Group]]:
+        all_groups: Optional[list[Group]] = Group.getAllGroups(con)
+        if all_groups:
+            project_groups = []
+            for group in all_groups:
+                if group.project == "http://rdfh.ch/projects/" + proj_shortcode:
+                    project_groups.append(group)
+            return project_groups
 
     def createDefinitionFileObj(self):
         group = {