SSX webservices

config/.env

@@ -10,3 +10,5 @@ TOKEN_EXP_TIME=300
 CORS=true
 
 AUTH_CONFIG=auth.yml
+
+PATH_MAP=${ISPYB_DATA_PATH}

config/ci.env

@@ -14,3 +14,5 @@ SECRET_KEY=ci_secret
 SQLALCHEMY_DATABASE_URI=mysql+mysqlconnector://test:test@127.0.0.1/test
 
 AUTH_CONFIG=tests/config/auth.yml
+
+PATH_MAP=${ISPYB_DATA_PATH}

config/dev.env

@@ -14,3 +14,5 @@ SECRET_KEY=dev_secret
 SQLALCHEMY_DATABASE_URI=mysql+mysqlconnector://test:test@127.0.0.1/test
 
 AUTH_CONFIG=auth.yml
+
+PATH_MAP=${ISPYB_DATA_PATH}

config/docker.env

@@ -10,3 +10,5 @@ TOKEN_EXP_TIME=300
 CORS=true
 
 AUTH_CONFIG=/config/auth.yml
+
+PATH_MAP=${ISPYB_DATA_PATH}

config/test.env

@@ -14,3 +14,5 @@ SECRET_KEY=test_secret
 SQLALCHEMY_DATABASE_URI=mysql+mysqlconnector://test:test@127.0.0.1/test
 
 AUTH_CONFIG=tests/config/auth.yml
+
+PATH_MAP=${ISPYB_DATA_PATH}

docs/conf.md

@@ -34,3 +34,7 @@ SQLALCHEMY_DATABASE_URI=mysql+mysqlconnector://test:test@127.0.0.1/test
 AUTH_CONFIG=auth.yml
 
 ```
+
+## ISPYB_DATA_PATH
+
+The env variable `ISPYB_DATA_PATH` allows you to define a path prefix that ISPyB should add to all data files path in the database.

pyispyb/app/base.py

@@ -14,9 +14,12 @@ def custom_generate_unique_id(route: APIRoute):
 
 class AuthenticatedAPIRouter(BaseRouter):
     def __init__(self, *args, **kwargs):
+
+        deps = kwargs.pop("dependencies", [])
+
         super().__init__(
             *args,
-            dependencies=[Depends(JWTBearer)],
+            dependencies=[Depends(JWTBearer), *deps],
             **kwargs,
             generate_unique_id_function=custom_generate_unique_id,
         )

pyispyb/app/utils/__init__.py

@@ -25,6 +25,8 @@
 from sqlalchemy import text
 from functools import wraps
 from pyispyb.config import settings
+from sqlalchemy.orm import class_mapper
+from sqlalchemy import inspect
 
 logger = logging.getLogger("ispyb")
 
@@ -87,3 +89,11 @@ def wrapper(self, *args, **kwargs):
         return result
 
     return wrapper
+
+
+def model_from_json(model, data):
+    mapper = class_mapper(model)
+    keys = mapper.attrs.keys()
+    relationships = inspect(mapper).relationships
+    args = {k: v for k, v in data.items() if k in keys and k not in relationships}
+    return model(**args)

pyispyb/core/modules/eventchains.py

@@ -0,0 +1,43 @@
+from sqlalchemy.orm import joinedload
+
+from ispyb import models
+
+from pyispyb.app.extensions.database.middleware import db
+from pyispyb.app.extensions.database.definitions import with_authorization
+from pyispyb.app.extensions.database.utils import Paged, page
+
+
+def get_datacollection_eventchains(
+    dataCollectionId: int,
+    skip: int,
+    limit: int,
+) -> list[models.EventChain]:
+    query = (
+        db.session.query(models.EventChain)
+        .filter(models.EventChain.dataCollectionId == dataCollectionId)
+        .options(joinedload(models.EventChain.events))
+        .join(
+            models.DataCollection,
+            models.EventChain.dataCollectionId
+            == models.DataCollection.dataCollectionId,
+        )
+        .join(
+            models.DataCollectionGroup,
+            models.DataCollection.dataCollectionGroupId
+            == models.DataCollectionGroup.dataCollectionGroupId,
+        )
+        .join(
+            models.BLSession,
+            models.DataCollectionGroup.sessionId == models.BLSession.sessionId,
+        )
+        .join(
+            models.Proposal, models.BLSession.proposalId == models.Proposal.proposalId
+        )
+    )
+
+    query = with_authorization(query, joinBLSession=False)
+
+    total = query.count()
+    query = page(query, skip=skip, limit=limit)
+
+    return Paged(total=total, results=query.all(), skip=skip, limit=limit)