refactor web app routes by mzouink · Pull Request #76 · janelia-cellmap/cellmap-flow

mzouink · 2026-02-11T19:58:49Z

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mzouink · 2026-02-11T19:59:17Z

Copilot

Pull request overview

This PR refactors the dashboard Flask app from a monolithic app.py into a blueprint-based route structure, introducing a shared state.py module for cross-route state (log streaming buffers, BBX generator state, and server URLs).

Changes:

Split dashboard endpoints into dedicated Flask blueprints under cellmap_flow/dashboard/routes/.
Added shared dashboard state in cellmap_flow/dashboard/state.py (log streaming + BBX generator state + configurable paths).
Updated the main dashboard app to register blueprints and wire up log streaming support.

Reviewed changes

Copilot reviewed 9 out of 10 changed files in this pull request and generated 18 comments.

Show a summary per file

File	Description
cellmap_flow/dashboard/app.py	Creates the Flask app, attaches a log handler, and registers all dashboard blueprints.
cellmap_flow/dashboard/state.py	Introduces shared global state (log buffers/clients, BBX generator state, and helper for blockwise task dir).
cellmap_flow/dashboard/routes/index_page.py	Serves the main index page and injects global state into templates.
cellmap_flow/dashboard/routes/pipeline_builder_page.py	Serves the pipeline builder UI and hydrates UI state from `g`.
cellmap_flow/dashboard/routes/pipeline.py	Adds pipeline APIs (apply/validate/process, dataset path, blockwise config).
cellmap_flow/dashboard/routes/models.py	Adds model catalog and model-config related APIs.
cellmap_flow/dashboard/routes/blockwise.py	Adds blockwise pipeline validation, YAML generation, precheck, and submission endpoints.
cellmap_flow/dashboard/routes/bbx_generator.py	Adds BBX generator endpoints backed by a Neuroglancer viewer.
cellmap_flow/dashboard/routes/logging_routes.py	Adds SSE log streaming and serves a bbox JSON template.
cellmap_flow/dashboard/routes/init.py	Package marker for routes.

Comments suppressed due to low confidence (1)

cellmap_flow/dashboard/app.py:48

create_and_run_app() sets port=0, which lets the OS choose an ephemeral port; without explicitly logging/returning the chosen port this can make the dashboard hard to discover/connect to. Consider using get_free_port() (as elsewhere in the repo) or a configurable fixed port, and log the final bind address for users.

    hostname = socket.gethostname()
    port = 0
    logger.warning(f"Host name: {hostname}")
    app.run(host="0.0.0.0", port=port, debug=False, use_reloader=False)

Copilot · 2026-02-11T20:06:53Z

+    input_norms = get_input_normalizers()
+    output_postprocessors = get_postprocessors_list()
+    model_mergers = get_model_mergers_list()
+    model_catalog = g.model_catalog


index() assigns model_catalog = g.model_catalog and then mutates it by adding a "User" category. This modifies global state for all subsequent requests and endpoints that use g.model_catalog. Consider copying (e.g., dict(g.model_catalog)) before adding request-specific entries.

Suggested change

model_catalog = g.model_catalog

model_catalog = dict(g.model_catalog)

Copilot · 2026-02-11T20:06:54Z

+        return {
+            "success": True,
+            "task_yaml": yaml_content,
+            "task_config": task_yaml,
+            "task_paths": yaml_paths,


When separate_bounding_boxes_zarrs is enabled, multiple bbox-specific YAML files are written, but the response still returns task_yaml/yaml_content from the base config. This means task_yaml/task_config won’t match the YAMLs referenced by task_paths. Consider returning per-bbox YAML/config (or a mapping of path->content) when generating multiple YAMLs.

Copilot · 2026-02-11T20:06:54Z

+                with viewer.txn() as s:
+                    try:
+                        annotations_layer = s.layers["annotations"]
+                        if hasattr(annotations_layer, 'annotations'):
+                            for ann in annotations_layer.annotations:


finalize_bbx_generation() reads s.layers["annotations"], but the layer created in start_bbx_generator() is named "bboxes". This prevents returning the final bounding boxes.

Copilot · 2026-02-11T20:06:54Z

+            model_entry = {
+                "name": model.get("name"),
+                **model.get("params", model.get("config", {}))


model_entry currently expands model.get("params", model.get("config", {})). If the frontend always includes a "params" key (even as an empty dict), the model's "config" will be ignored and the generated YAML will miss required model configuration. Prefer merging config+params (with params overriding) or falling back to config when params is empty.

Suggested change

model_entry = {

"name": model.get("name"),

**model.get("params", model.get("config", {}))

config = model.get("config") or {}

if not isinstance(config, dict):

config = {}

params = model.get("params")

if not params:

combined_params = config

else:

if not isinstance(params, dict):

params = {}

combined_params = {**config, **params}

model_entry = {

"name": model.get("name"),

**combined_params

Copilot · 2026-02-11T20:06:54Z

+        if not pipeline.get("inputs") or len(pipeline["inputs"]) == 0:
+            return {"valid": False, "error": "No input nodes defined"}
+
+        if not pipeline.get("outputs") or len(pipeline["outputs"]) == 0:
+            return {"valid": False, "error": "No output nodes defined"}


This validation route returns plain dicts (defaulting to HTTP 200) even for validation failures. For an API endpoint, return jsonify(...) and use 4xx status codes for invalid pipelines so client-side error handling is reliable.

Copilot · 2026-02-11T20:06:57Z

+                with viewer.txn() as s:
+                    try:
+                        annotations_layer = s.layers["annotations"]
+                        if hasattr(annotations_layer, 'annotations'):
+                            for ann in annotations_layer.annotations:


The viewer creates an annotation layer named "bboxes", but status extraction reads from s.layers["annotations"]. This will raise KeyError and prevent returning any bounding boxes. Read from the same layer name that was created ("bboxes").

Copilot · 2026-02-11T20:06:57Z

+        # Build bsub command
+        cores_master = blockwise_config["params"]["nb_cores_master"]
+        charge_group = blockwise_config["params"]["charge_group"]
+        queue = blockwise_config["params"]["queue"]


Variable queue is not used.

Suggested change

queue = blockwise_config["params"]["queue"]

Copilot · 2026-02-11T20:06:57Z

+
+
+@logging_bp.route("/api/templates/bbox-json")
+def get_bbox_json_template():


get_bbox_json_template returns tuple of size 2 and tuple of size 3.

Copilot · 2026-02-11T20:06:58Z

+import yaml
+from flask import Blueprint, request
+
+from cellmap_flow.globals import g


Import of 'g' is not used.

Suggested change

from cellmap_flow.globals import g

Copilot · 2026-02-11T20:06:58Z

+        for client_queue in log_clients:
+            try:
+                client_queue.put_nowait(log_entry)
+            except queue.Full:


'except' clause does nothing but pass and there is no explanatory comment.

Suggested change

except queue.Full:

except queue.Full:

# Intentionally drop log entries when a client's queue is full.

# Logging should never block or raise due to slow consumers.

refactor routes

03a48ea

Copilot AI review requested due to automatic review settings February 11, 2026 19:58

Merge branch 'main' into refactor_web_app

5100927

Copilot started reviewing on behalf of mzouink February 11, 2026 19:59 View session

mzouink merged commit 38160e0 into main Feb 11, 2026

mzouink deleted the refactor_web_app branch February 11, 2026 19:59

Copilot AI reviewed Feb 11, 2026

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refactor web app routes#76

refactor web app routes#76
mzouink merged 2 commits intomainfrom
refactor_web_app

mzouink commented Feb 11, 2026

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	model_catalog = g.model_catalog
	model_catalog = dict(g.model_catalog)

-            model_entry = {
-                "name": model.get("name"),
-                **model.get("params", model.get("config", {}))
+            config = model.get("config") or {}
+            if not isinstance(config, dict):
+                config = {}
+            params = model.get("params")
+            if not params:
+                combined_params = config
+            else:
+                if not isinstance(params, dict):
+                    params = {}
+                combined_params = {**config, **params}
+            model_entry = {
+                "name": model.get("name"),
+                **combined_params



		@logging_bp.route("/api/templates/bbox-json")
		def get_bbox_json_template():

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mzouink commented Feb 11, 2026

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