Merge remote-tracking branch 'upstream/datajoint_pipeline' into dataj…

…oint_pipeline
SainsburyWellcomeCentre · Apr 4, 2024 · e6ed4af · e6ed4af
2 parents 28e5397 + b8f76d4
commit e6ed4af
Show file tree

Hide file tree

Showing 5 changed files with 718 additions and 13 deletions.
diff --git a/aeon/dj_pipeline/analysis/block_analysis.py b/aeon/dj_pipeline/analysis/block_analysis.py
@@ -8,8 +8,10 @@
 from matplotlib import path as mpl_path
 
 from aeon.analysis import utils as analysis_utils
-from aeon.dj_pipeline import acquisition, fetch_stream, get_schema_name, streams, tracking
-from aeon.dj_pipeline.analysis.visit import filter_out_maintenance_periods, get_maintenance_periods
+from aeon.dj_pipeline import (acquisition, fetch_stream, get_schema_name,
+                              streams, tracking)
+from aeon.dj_pipeline.analysis.visit import (filter_out_maintenance_periods,
+                                             get_maintenance_periods)
 
 schema = dj.schema(get_schema_name("block_analysis"))
 logger = dj.logger
@@ -516,7 +518,7 @@ def make(self, key):
         )
 
         block_query = acquisition.Environment.BlockState & chunk_restriction
-        block_df = fetch_stream(block_query)[previous_block_start:chunk_end]
+        block_df = fetch_stream(block_query).sort_index()[previous_block_start:chunk_end]
 
         block_ends = block_df[block_df.pellet_ct.diff() < 0]
 

diff --git a/aeon/dj_pipeline/webapps/sciviz/README.md b/aeon/dj_pipeline/webapps/sciviz/README.md
@@ -26,7 +26,7 @@ HOST_UID=$(id -u) docker-compose -f docker-compose-local.yaml up
 ```
 
 #### Verify the deployment
-- In your web browser, navigate to: [https://localhost/login](https://localhost/login)
+- In your web browser, navigate to: [https://localhost/](https://localhost/)
 - Set `Username` and `Password` to your own database user account (if you need one, please contact Project Aeon admin team).
 - Click `Connect`.
 - To stop the application, docker compose down with the following:
@@ -52,7 +52,8 @@ HOST_UID=$(id -u) docker-compose -f docker-compose-remote.yaml up -d
 
 ---
 ## Dynamic spec sheet
-Sci-Viz is used to build visualization dashboards, this is done through a single spec sheet. The one for this deployment is called `specsheet.yaml`
+Sci-Viz is used to build visualization dashboards, this is done through a single spec sheet. The one used in production is called `specsheet.yaml`,
+and the one used locally is called `specsheet-local.yaml`.
 
 Some notes about the spec sheet if you plan to tweak the website yourself:
 - Page names under pages must have a unique name without spaces

diff --git a/aeon/dj_pipeline/webapps/sciviz/docker-compose-local.yaml b/aeon/dj_pipeline/webapps/sciviz/docker-compose-local.yaml
@@ -7,14 +7,14 @@ services:
   pharus:
     cpus: 2.0
     mem_limit: 4g
-    image: jverswijver/pharus:0.8.5-PY_VER-3.9
+    image: datajoint/pharus:0.8.10-py3.9
     environment:
       # - FLASK_ENV=development # enables logging to console from Flask
-      - PHARUS_SPEC_PATH=/main/specsheet.yaml # for dynamic utils spec
+      - PHARUS_SPEC_PATH=/main/specsheet-local.yaml # for dynamic utils spec
       - PHARUS_MODE=DEV
     user: root
     volumes:
-      - ./specsheet.yaml:/main/specsheet.yaml #copy the spec over to /main/specs/YOUR_SPEC_NAME
+      - ./specsheet-local.yaml:/main/specsheet-local.yaml #copy the spec over to /main/specs/YOUR_SPEC_NAME
       - ./apk_requirements.txt:/tmp/apk_requirements.txt
       - /ceph/aeon/aeon:/ceph/aeon/aeon
     command:
@@ -23,12 +23,12 @@ services:
       - |
         apk add --update git g++ &&
         git clone -b datajoint_pipeline https://github.com/SainsburyWellcomeCentre/aeon_mecha.git &&
-        pip install -e ./aeon_mecha &&
+        pip install -e ./aeon_mecha --ignore-requires-python &&
         pharus_update() {
             [ -z "$$GUNICORN_PID" ] || kill $$GUNICORN_PID
             gunicorn --bind 0.0.0.0:$${PHARUS_PORT} pharus.server:app &
             GUNICORN_PID=$$!
-        }
+        } &&
         pharus_update
         echo "[$$(date -u '+%Y-%m-%d %H:%M:%S')][DataJoint]: Monitoring Pharus updates..."
         INIT_TIME=$$(date +%s)
@@ -52,16 +52,16 @@ services:
   sci-viz:
     cpus: 2.0
     mem_limit: 16g
-    image: jverswijver/sci-viz:2.3.3-hotfix3
+    image: jverswijver/sci-viz:2.3.5-beta
     environment:
       - CHOKIDAR_USEPOLLING=true
       - REACT_APP_DJSCIVIZ_BACKEND_PREFIX=/api
-      - DJSCIVIZ_SPEC_PATH=/main/specsheet.yaml
+      - DJSCIVIZ_SPEC_PATH=/main/specsheet-local.yaml
       - DJSCIVIZ_MODE=DEV
       - NODE_OPTIONS="--max-old-space-size=12000"
     user: root
     volumes:
-      - ./specsheet.yaml:/main/specsheet.yaml
+      - ./specsheet-local.yaml:/main/specsheet-local.yaml
     # ports:
     #   - "3000:3000"
     command: