From 1d0dc25323c5dd123e80e31605e11579bb0d1718 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Thu, 25 May 2023 12:31:53 +0200
Subject: [PATCH 1/4] fix: fix voluba web service reference

---
 .../voluba_backend/ebrains_router/models.py   |  8 +-
 .../voluba_webservice_jsonld.json             | 90 +++++++++++++++++++
 2 files changed, 97 insertions(+), 1 deletion(-)
 create mode 100644 backend/voluba_backend/ebrains_router/voluba_webservice_jsonld.json

diff --git a/backend/voluba_backend/ebrains_router/models.py b/backend/voluba_backend/ebrains_router/models.py
index 8e106d9e..5e4c5e22 100644
--- a/backend/voluba_backend/ebrains_router/models.py
+++ b/backend/voluba_backend/ebrains_router/models.py
@@ -12,6 +12,7 @@
 from hashlib import md5
 from datetime import datetime
 import requests
+from pathlib import Path
 
 from voluba_auth import S2SToken
 from .const import SPC_NAME_TO_ID_VOCAB, KG_INSTANCES, KG_IDS, SPC_NAME_TO_KG_ID, STRING_CONST
@@ -127,7 +128,12 @@ def _run(self, context: 'WorkProgress'):
         auth_token = S2SToken.get_token()
         kg_client = KGClient(auth_token, host=KG_ROOT)
         if KG_INSTANCES.voluba_webservice_version is None:
-            KG_INSTANCES.voluba_webservice_version = WebServiceVersion.from_id(KG_IDS.VOLUBA_WEBSERVICE_VERSION_ID, kg_client, scope="any")
+            # TODO s2s token cannot seem to query instances in review space
+            # personal tokens do not suffer from this limitation, which is why on webUI, everything seems fine
+            # for now, load the jsonld (fetched and saved while using a personal token)
+            path_to_jsonld = Path(__file__).parent / "voluba_webservice_jsonld.json",
+            with open(path_to_jsonld, "r") as fp:
+                KG_INSTANCES.voluba_webservice_version = WebServiceVersion.from_jsonld(json.load(fp=fp), kg_client)
         
         assert context.param.reference_volume in SPC_NAME_TO_KG_ID, f"Expecting reference volume {context.param.reference_volume!r} be in {', '.join(SPC_NAME_TO_KG_ID.keys())}, but is not."
 
diff --git a/backend/voluba_backend/ebrains_router/voluba_webservice_jsonld.json b/backend/voluba_backend/ebrains_router/voluba_webservice_jsonld.json
new file mode 100644
index 00000000..3f84c426
--- /dev/null
+++ b/backend/voluba_backend/ebrains_router/voluba_webservice_jsonld.json
@@ -0,0 +1,90 @@
+{
+	"@type": [
+		"https://openminds.ebrains.eu/core/WebServiceVersion"
+	],
+	"@id": "https://kg.ebrains.eu/api/instances/eb1eb844-3544-45cf-829e-1094225d0007",
+	"https://openminds.ebrains.eu/vocab/fullName": "VoluBA - Volumetric Brain Anchoring",
+	"https://openminds.ebrains.eu/vocab/shortName": "VoluBA",
+	"https://openminds.ebrains.eu/vocab/accessibility": {
+		"@id": "https://kg.ebrains.eu/api/instances/f1389b7e-0965-4d23-9ddb-2575d4ac2fad"
+	},
+	"https://openminds.ebrains.eu/vocab/copyright": {
+		"@type": [
+			"https://openminds.ebrains.eu/core/Copyright"
+		],
+		"https://openminds.ebrains.eu/vocab/holder": {
+			"@id": "https://kg.ebrains.eu/api/instances/561a0c75-a414-45b0-a24e-e2f8e680ec2e"
+		},
+		"https://openminds.ebrains.eu/vocab/year": "2017"
+	},
+	"https://openminds.ebrains.eu/vocab/fullDocumentation": {
+		"@id": "https://kg.ebrains.eu/api/instances/12aa623f-0313-4ab0-919a-d8e5c6afdad0"
+	},
+	"https://openminds.ebrains.eu/vocab/funding": [
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/586250ba-571d-4a14-813a-d997c500e9f7"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/754aeb36-9420-4484-9b50-6ca0eb806a0d"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/082a5bf9-1612-4a44-9b19-d6757a0a83ec"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/7c0695e3-2031-49d9-9253-d07c9db2d230"
+		}
+	],
+	"https://openminds.ebrains.eu/vocab/hasPart": {
+		"@id": "https://kg.ebrains.eu/api/instances/7a77ccdb-c62d-42a4-a373-a47619d34e74"
+	},
+	"https://openminds.ebrains.eu/vocab/homepage": "https://voluba.apps.hbp.eu/#/",
+	"https://openminds.ebrains.eu/vocab/inputFormat": [
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/f7c21b4d-b27d-4a5c-b184-d2aa66100466"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/f9099808-731f-453e-8e81-404ec482a721"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/ee347aa2-4746-44e7-968a-467d04e4969d"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/caeef910-8691-4e88-83a0-726ea844c2d9"
+		}
+	],
+	"https://openminds.ebrains.eu/vocab/keyword": [
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/21d46eb1-7933-4418-98af-d3d92d9babe3"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/4d294fe1-5cbe-4ae4-bcdc-88866798550b"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/f04a66d9-9c24-4076-84cd-155607587fa0"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/dadd102a-2472-40b0-a500-be168bd6b64f"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/5a2fb93a-e5ab-4638-b1fc-065dd49506dc"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/4ccfa2b8-fe75-4a17-98b7-e01b922c8f03"
+		}
+	],
+	"https://openminds.ebrains.eu/vocab/outputFormat": [
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/ee347aa2-4746-44e7-968a-467d04e4969d"
+		},
+		{
+			"@id": "https://kg.ebrains.eu/api/instances/caeef910-8691-4e88-83a0-726ea844c2d9"
+		}
+	],
+	"https://openminds.ebrains.eu/vocab/releaseDate": "2020-01-04T00:00:00",
+	"https://openminds.ebrains.eu/vocab/repository": {
+		"@id": "https://kg.ebrains.eu/api/instances/f9a4d451-0c39-424f-9b0e-e903ee6fdf8a"
+	},
+	"https://openminds.ebrains.eu/vocab/supportChannel": "support@ebrains.eu",
+	"https://openminds.ebrains.eu/vocab/versionIdentifier": "v0",
+	"https://openminds.ebrains.eu/vocab/versionInnovation": "This version has no official release on GitHub. VoluBA was previously known as landmark-reg."
+}
\ No newline at end of file

From 4c10216dfbc4a53a3c33e080674e115cf5d9fdca Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Thu, 25 May 2023 12:46:21 +0200
Subject: [PATCH 2/4] feat: allow user to add desc

---
 app/src/components/exports/ExportsEbrains.vue      | 14 +++++++++++++-
 backend/voluba_backend/.gitignore                  |  1 +
 backend/voluba_backend/ebrains_router/models.py    |  5 ++++-
 .../siibra_explorer_overlay/__init__.py            |  8 +++++++-
 4 files changed, 25 insertions(+), 3 deletions(-)
 create mode 100644 backend/voluba_backend/.gitignore

diff --git a/app/src/components/exports/ExportsEbrains.vue b/app/src/components/exports/ExportsEbrains.vue
index 06047971..0392a861 100644
--- a/app/src/components/exports/ExportsEbrains.vue
+++ b/app/src/components/exports/ExportsEbrains.vue
@@ -1,5 +1,12 @@
 <template>
   <div>
+    <b-form-textarea v-model="description"
+      :aria-placeholder="descriptionPlaceholder"
+      :placeholder="descriptionPlaceholder"
+      class="mb-2">
+
+    </b-form-textarea>
+    <div></div>
     <b-button @click="start"
       :disabled="isBusy"
       class="start-button"
@@ -32,6 +39,8 @@ export default {
       pollResults: [],
       jobId: null,
       periodicId: null,
+      description: '',
+      descriptionPlaceholder: '(Optional) Enter a description for this transformation.',
     }
   },
   filters: {
@@ -59,7 +68,10 @@ export default {
       try {
         const resp = await fetch(`${hostname}ebrains`, {
           method: 'POST',
-          body: JSON.stringify(json),
+          body: JSON.stringify({
+            ...json,
+            description: this.description
+          }),
           headers: {
             'content-type': 'application/json'
           }
diff --git a/backend/voluba_backend/.gitignore b/backend/voluba_backend/.gitignore
new file mode 100644
index 00000000..4c49bd78
--- /dev/null
+++ b/backend/voluba_backend/.gitignore
@@ -0,0 +1 @@
+.env
diff --git a/backend/voluba_backend/ebrains_router/models.py b/backend/voluba_backend/ebrains_router/models.py
index 5e4c5e22..fe5ce540 100644
--- a/backend/voluba_backend/ebrains_router/models.py
+++ b/backend/voluba_backend/ebrains_router/models.py
@@ -31,6 +31,7 @@ class WorkflowV1_1(BaseModel):
     version: Union[int, float, str]
     _type:str = Field(..., alias="@type")
     transform_matrix_in_nm: List[List[float]] = Field(..., alias="transformMatrixInNm")
+    description: str = ''
 
 class StartWorkflowResp(BaseModel):
     job_id: str
@@ -162,7 +163,9 @@ def _run(self, context: 'WorkProgress'):
             outputs=[
                 output_file
             ],
-            description="Programmatically generated by voluba by way of fairgraph.",
+            description=f"""{context.param.description}
+
+Programmatically generated by voluba by way of fairgraph.""",
             start_time=datetime.now()
         )
         da.save(kg_client, KG_SPACE_NAME)
diff --git a/backend/voluba_backend/siibra_explorer_overlay/__init__.py b/backend/voluba_backend/siibra_explorer_overlay/__init__.py
index 2da3e2ee..c62e1723 100644
--- a/backend/voluba_backend/siibra_explorer_overlay/__init__.py
+++ b/backend/voluba_backend/siibra_explorer_overlay/__init__.py
@@ -1,5 +1,6 @@
 from fastapi import APIRouter, Response
 from pathlib import Path
+from typing import List
 import json
 
 with open(Path(__file__).parent / 'template.html', 'r') as fp:
@@ -10,7 +11,12 @@
 def islen(num: int):
     return lambda variable: isinstance(variable, list) and len(variable) == num
 
-def verify_transform(transform: str):
+def verify_transform(transform: str) -> List[List[float]]:
+    """
+    transform is provided as a str of 12 comma separated floats,
+    reshaped to 4x3 row major affine.
+    This function checks the validity and returns the actual affine.
+    """
     return_result = [float(v) for v in transform.split(",")]
     assert islen(12)(return_result)
     return [

From 79aae70987cdb35879a2b2bd4725665a92c7973b Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Thu, 25 May 2023 14:45:52 +0200
Subject: [PATCH 3/4] feat: add user to performed by

---
 .../voluba_backend/ebrains_router/models.py   | 48 ++++++++++++++++++-
 .../voluba_backend/ebrains_router/router.py   | 10 ++--
 backend/voluba_backend/voluba_auth.py         | 12 ++++-
 3 files changed, 62 insertions(+), 8 deletions(-)

diff --git a/backend/voluba_backend/ebrains_router/models.py b/backend/voluba_backend/ebrains_router/models.py
index fe5ce540..927f23b4 100644
--- a/backend/voluba_backend/ebrains_router/models.py
+++ b/backend/voluba_backend/ebrains_router/models.py
@@ -1,4 +1,4 @@
-from typing import Union, List, Optional, Callable
+from typing import Union, List, Optional, Callable, Literal
 from enum import Enum
 from pydantic import BaseModel, Field
 from tempfile import NamedTemporaryFile
@@ -8,6 +8,7 @@
 from fairgraph.openminds.core import ContentType, File, WebServiceVersion, Hash
 from fairgraph.openminds.sands import CommonCoordinateSpaceVersion
 from fairgraph.openminds.computation import LocalFile, DataAnalysis
+from fairgraph.openminds.core.actors.person import Person
 import json
 from hashlib import md5
 from datetime import datetime
@@ -148,7 +149,9 @@ def _run(self, context: 'WorkProgress'):
 
         ref_spc_kg_id = SPC_NAME_TO_KG_ID[context.param.reference_volume]
         spc = CommonCoordinateSpaceVersion.from_id(ref_spc_kg_id, client=kg_client)
-        
+
+        user = context.user.fetch_kg_instance()
+
         lookup_label=f"{context.param.reference_volume}-{context.param.incoming_volume}"
         input_file = LocalFile.from_id(income_vol_local_file.detail, client=kg_client, scope="any")
         output_file = File.from_id(transform_file.detail, client=kg_client, scope="any")
@@ -163,6 +166,7 @@ def _run(self, context: 'WorkProgress'):
             outputs=[
                 output_file
             ],
+            performed_by=[user],
             description=f"""{context.param.description}
 
 Programmatically generated by voluba by way of fairgraph.""",
@@ -191,11 +195,51 @@ def _run(self, context: 'WorkProgress'):
             print(errors)
             raise Exception(f"Some instances cannot be deleted: {','.join([err.get('id') for err in errors])}")
 
+
+class VolubaUser(BaseModel):
+    id: str
+    name: str
+    given_name: str
+    family_name: str
+    type: Union[Literal['hbp-oidc-v2'], Literal['orcid-oidc']]
+
+    def fetch_kg_instance(self) -> Person:
+        auth_token = S2SToken.get_token()
+        kg_client = KGClient(auth_token, host=KG_ROOT)
+        
+        p = Person(family_name=self.family_name, given_name=self.given_name)
+        query = Person.generate_query(client=kg_client, space=None, filters=p._build_existence_query())
+        q = kg_client.query(
+            query=query,
+            size=100,
+            scope="any"
+        )
+        persons = [Person.from_jsonld(d, kg_client) for d in q.data]
+        if self.type == "hbp-oidc-v2":
+            persons = [p for p in persons if p.space == "common"]
+            if len(persons) == 1:
+                return persons[0]
+            raise Exception(f"User not found, or multiple users found: {len(persons)}")
+        if self.type == "orcid-oidc":
+            persons = [p for p in persons
+                       if p.space == "collab-spatial-anchoring"
+                       and self.id in p.alternate_names]
+            if len(persons) == 0:
+                p = Person(family_name=self.family_name, given_name=self.given_name, alternate_names=["voluba-created", self.type, self.id])
+                p.save(kg_client, KG_SPACE_NAME)
+                return p
+            if len(persons) == 1:
+                return persons[0]
+            raise Exception(f"Multiple user found: {len(persons)}")
+        
+        raise Exception(f"type must be orcid-oidc or hbp-oidc-v2")
+    
 class WorkProgress(BaseModel):
     id: str
     param: WorkflowV1_1
     output_hash: str=None
     progresses: List[JobProgressModel]
+    user: Optional[VolubaUser]=None
 
     def get_ooo(self, fn: Callable[[JobProgressModel], bool]) -> JobProgressModel:
         """
diff --git a/backend/voluba_backend/ebrains_router/router.py b/backend/voluba_backend/ebrains_router/router.py
index 99cb6706..bf10a268 100644
--- a/backend/voluba_backend/ebrains_router/router.py
+++ b/backend/voluba_backend/ebrains_router/router.py
@@ -1,6 +1,6 @@
 from voluba_store import VolubaStore
 
-from .models import StartWorkflowResp, WorkflowV1_1, WorkProgress, UploadToDP, CreateKgTransformFileInstance, CreateKgIncVolFileInstance, CreateKgDataAnalysisInstance
+from .models import StartWorkflowResp, WorkflowV1_1, WorkProgress, UploadToDP, CreateKgTransformFileInstance, CreateKgIncVolFileInstance, CreateKgDataAnalysisInstance, VolubaUser
 
 from uuid import uuid4
 from fastapi import APIRouter, Request, BackgroundTasks, Cookie, Depends
@@ -13,10 +13,11 @@
 
 router = APIRouter()
 
-# TODO add check that user is authenticated
-
 @router.post("", response_model=StartWorkflowResp)
 def start_workflow(body: WorkflowV1_1, request: Request, bg: BackgroundTasks):
+    user = get_user(request)
+    if not user:
+        raise HTTPException(401, detail="You need to be authenticated to use this endpoint.")
     job_id = str(uuid4())
     result=StartWorkflowResp(job_id=job_id)
     work=WorkProgress(
@@ -27,7 +28,8 @@ def start_workflow(body: WorkflowV1_1, request: Request, bg: BackgroundTasks):
             CreateKgTransformFileInstance(),
             CreateKgIncVolFileInstance(),
             CreateKgDataAnalysisInstance(),
-        ]
+        ],
+        user=VolubaUser(**user)
     )
     worflow_store.set_value(job_id, work)
     bg.add_task(work.start)
diff --git a/backend/voluba_backend/voluba_auth.py b/backend/voluba_backend/voluba_auth.py
index fc849e42..f7c49b73 100644
--- a/backend/voluba_backend/voluba_auth.py
+++ b/backend/voluba_backend/voluba_auth.py
@@ -46,9 +46,13 @@
 
 def process_hbp_user(resp):
     userinfo = resp.get("userinfo")
+    given_name = userinfo.get("given_name")
+    family_name = userinfo.get("family_name")
     return {
         'id': f'hbp-oidc-v2:{userinfo.get("sub")}',
-        'name': f'{userinfo.get("given_name")} {userinfo.get("family_name")}',
+        'name': f'{given_name} {family_name}',
+        'given_name': given_name,
+        'family_name': family_name,
         'type': 'hbp-oidc-v2',
         'idToken': resp.get("id_token"),
         'accessToken': resp.get("access_token"),
@@ -74,9 +78,13 @@ async def ebrains_callback(request: Request):
 
 def process_orcid_user(resp):
     userinfo = resp.get("userinfo")
+    given_name = userinfo.get("given_name")
+    family_name = userinfo.get("family_name")
     return {
         'id': f'orcid:{userinfo.get("sub")}',
-        'name': f'{userinfo.get("given_name")} {userinfo.get("family_name")}',
+        'name': f'{given_name} {family_name}',
+        'given_name': given_name,
+        'family_name': family_name,
         'type': 'orcid-oidc',
         'idToken': resp.get("id_token"),
         'accessToken': resp.get("access_token"),

From 4486866ad722d4891389e1f62f7cfaa2ebf113a2 Mon Sep 17 00:00:00 2001
From: Xiao Gui <xgui3783@gmail.com>
Date: Thu, 25 May 2023 15:01:42 +0200
Subject: [PATCH 4/4] maint: add differentiator to filename

---
 backend/voluba_backend/ebrains_router/models.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/backend/voluba_backend/ebrains_router/models.py b/backend/voluba_backend/ebrains_router/models.py
index 927f23b4..9ff2f275 100644
--- a/backend/voluba_backend/ebrains_router/models.py
+++ b/backend/voluba_backend/ebrains_router/models.py
@@ -14,6 +14,7 @@
 from datetime import datetime
 import requests
 from pathlib import Path
+from uuid import uuid4
 
 from voluba_auth import S2SToken
 from .const import SPC_NAME_TO_ID_VOCAB, KG_INSTANCES, KG_IDS, SPC_NAME_TO_KG_ID, STRING_CONST
@@ -65,11 +66,13 @@ def _run(self, context: 'WorkProgress'):
         auth_token = S2SToken.get_token()
         client = BucketApiClient(token=auth_token)
         bucket = client.buckets.get_bucket(DP_BUCKET_NAME)
+
+        _id = str(uuid4())
         
         assert context.param.reference_volume in SPC_NAME_TO_ID_VOCAB, f"Expecting reference volume name {context.param.reference_volume} is in {', '.join(SPC_NAME_TO_ID_VOCAB.keys())}, but is not."
         sanitized_spc_id = SPC_NAME_TO_ID_VOCAB[context.param.reference_volume].replace("/", ".")
         incoming_vol_id = context.param.content_hash or f'name.{context.param.incoming_volume}'
-        bucket_filename = f"{sanitized_spc_id}_{incoming_vol_id}_transform_{context.param.version}.json"
+        bucket_filename = f"{sanitized_spc_id}_{incoming_vol_id}_transform_{context.param.version}_{_id}.json"
 
         # Unfortunately, bucket API does not yet support stringIO, and must write it to disk first.
         with NamedTemporaryFile("w", suffix=".json", encoding="utf-8", delete=False) as fp: