Merge pull request #90 from MilagrosMarin/element-dlc-test

Update the example data, environment variables, tutorial notebook and README

.devcontainer/Dockerfile

@@ -42,9 +42,12 @@ ENV DJ_HOST fakeservices.datajoint.io
 ENV DJ_USER root
 ENV DJ_PASS simple
 
-ENV DLC_ROOT_DATA_DIR /workspaces/element-deeplabcut/example_data
-ENV CURRENT_PROJECT_FOLDER from_top_tracking
+ENV DATA_MOUNTPOINT /workspaces/element-deeplabcut/example_data
+ENV DLC_ROOT_DATA_DIR $DATA_MOUNTPOINT/inbox
+ENV DLC_PROCESSED_DATA_DIR $DATA_MOUNTPOINT/outbox
 ENV DATABASE_PREFIX neuro_
 
 USER vscode
-CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"
+CMD bash -c "sudo rm /var/run/docker.pid; sudo dockerd"
+
+ENV LD_LIBRARY_PATH="/lib:/opt/conda/lib"

.devcontainer/devcontainer.json

@@ -6,8 +6,8 @@
 	"remoteEnv": {
 		"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
 	},
-	"onCreateCommand": "mkdir -p ${DLC_ROOT_DATA_DIR} && pip install -e .",
-	"postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${DLC_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
+	"onCreateCommand": "mkdir -p ${DATA_MOUNTPOINT} && pip install -e .",
+	"postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${DATA_MOUNTPOINT} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
 	"hostRequirements": {
 		"cpus": 4,
 		"memory": "8gb",

.devcontainer/docker-compose.yaml

@@ -10,7 +10,7 @@ services:
     extra_hosts:
       - fakeservices.datajoint.io:127.0.0.1
     environment:
-      - DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-dlc-data/v1
+      - DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-dlc-data/v2
     devices:
       - /dev/fuse
     cap_add:

README.md

@@ -14,7 +14,7 @@ tables that can be combined with other Elements to assemble a fully functional p
 
 ## Data Pipeline Diagram
 
-![pipeline](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/pipeline_dlc.svg)
+![pipeline](https://raw.githubusercontent.com/datajoint/element-deeplabcut/main/images/pipeline.svg)
 
 ## Getting Started
 

element_deeplabcut/__init__.py

@@ -14,7 +14,8 @@
     "DLC_ROOT_DATA_DIR", dj.config["custom"].get("dlc_root_data_dir", "")
 )
 
-dj.config["custom"]["current_project_folder"] = os.getenv(
-    "CURRENT_PROJECT_FOLDER", dj.config["custom"].get("current_project_folder", "")
+dj.config["custom"]["dlc_processed_data_dir"] = os.getenv(
+    "DLC_PROCESSED_DATA_DIR", dj.config["custom"].get("dlc_processed_data_dir", "")
 )
+
 db_prefix = dj.config["custom"].get("database.prefix", "")

element_deeplabcut/model.py

@@ -453,7 +453,10 @@ def insert_new_model(
             print("Canceled insert.")
             return
         # ---- Save DJ-managed config ----
-        _ = dlc_reader.save_yaml(project_path, dlc_config)
+        try:
+            _ = dlc_reader.save_yaml(project_path, dlc_config)
+        except PermissionError:
+            pass
         # ____ Insert into table ----
         with cls.connection.transaction:
             cls.insert1(model_dict)