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feat: Add Studio UI, intake system, and extractor improvements

Browse Source 
Dashboard:
- Add Studio page with drag-drop model upload and Claude chat
- Add intake system for study creation workflow
- Improve session manager and context builder
- Add intake API routes and frontend components

Optimization Engine:
- Add CLI module for command-line operations
- Add intake module for study preprocessing
- Add validation module with gate checks
- Improve Zernike extractor documentation
- Update spec models with better validation
- Enhance solve_simulation robustness

Documentation:
- Add ATOMIZER_STUDIO.md planning doc
- Add ATOMIZER_UX_SYSTEM.md for UX patterns
- Update extractor library docs
- Add study-readme-generator skill

Tools:
- Add test scripts for extraction validation
- Add Zernike recentering test

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
Anto01
2026-01-27 12:02:30 -05:00
parent 3193831340
commit a26914bbe8
56 changed files with 14173 additions and 646 deletions
Download Patch File Download Diff File Expand all files Collapse all files

256
atomizer-dashboard/backend/api/services/spec_manager.py
View File

@@ -47,11 +47,13 @@ from optimization_engine.config.spec_validator import (
class SpecManagerError(Exception):
"""Base error for SpecManager operations."""
pass
class SpecNotFoundError(SpecManagerError):
"""Raised when spec file doesn't exist."""
pass
@@ -118,7 +120,7 @@ class SpecManager:
if not self.spec_path.exists():
raise SpecNotFoundError(f"Spec not found: {self.spec_path}")
with open(self.spec_path, 'r', encoding='utf-8') as f:
with open(self.spec_path, "r", encoding="utf-8") as f:
data = json.load(f)
if validate:
@@ -141,14 +143,15 @@ class SpecManager:
if not self.spec_path.exists():
raise SpecNotFoundError(f"Spec not found: {self.spec_path}")
with open(self.spec_path, 'r', encoding='utf-8') as f:
with open(self.spec_path, "r", encoding="utf-8") as f:
return json.load(f)
def save(
self,
spec: Union[AtomizerSpec, Dict[str, Any]],
modified_by: str = "api",
expected_hash: Optional[str] = None
expected_hash: Optional[str] = None,
skip_validation: bool = False,
) -> str:
"""
Save spec with validation and broadcast.
@@ -157,6 +160,7 @@ class SpecManager:
spec: Spec to save (AtomizerSpec or dict)
modified_by: Who/what is making the change
expected_hash: If provided, verify current file hash matches
skip_validation: If True, skip strict validation (for draft specs)
Returns:
New spec hash
@@ -167,7 +171,7 @@ class SpecManager:
"""
# Convert to dict if needed
if isinstance(spec, AtomizerSpec):
data = spec.model_dump(mode='json')
data = spec.model_dump(mode="json")
else:
data = spec
@@ -176,24 +180,30 @@ class SpecManager:
current_hash = self.get_hash()
if current_hash != expected_hash:
raise SpecConflictError(
"Spec was modified by another client",
current_hash=current_hash
"Spec was modified by another client", current_hash=current_hash
)
# Update metadata
now = datetime.now(timezone.utc).isoformat().replace('+00:00', 'Z')
now = datetime.now(timezone.utc).isoformat().replace("+00:00", "Z")
data["meta"]["modified"] = now
data["meta"]["modified_by"] = modified_by
# Validate
self.validator.validate(data, strict=True)
# Validate (skip for draft specs or when explicitly requested)
status = data.get("meta", {}).get("status", "draft")
is_draft = status in ("draft", "introspected", "configured")
if not skip_validation and not is_draft:
self.validator.validate(data, strict=True)
elif not skip_validation:
# For draft specs, just validate non-strictly (collect warnings only)
self.validator.validate(data, strict=False)
# Compute new hash
new_hash = self._compute_hash(data)
# Atomic write (write to temp, then rename)
temp_path = self.spec_path.with_suffix('.tmp')
with open(temp_path, 'w', encoding='utf-8') as f:
temp_path = self.spec_path.with_suffix(".tmp")
with open(temp_path, "w", encoding="utf-8") as f:
json.dump(data, f, indent=2, ensure_ascii=False)
temp_path.replace(self.spec_path)
@@ -202,12 +212,9 @@ class SpecManager:
self._last_hash = new_hash
# Broadcast to subscribers
self._broadcast({
"type": "spec_updated",
"hash": new_hash,
"modified_by": modified_by,
"timestamp": now
})
self._broadcast(
{"type": "spec_updated", "hash": new_hash, "modified_by": modified_by, "timestamp": now}
)
return new_hash
@@ -219,7 +226,7 @@ class SpecManager:
"""Get current spec hash."""
if not self.spec_path.exists():
return ""
with open(self.spec_path, 'r', encoding='utf-8') as f:
with open(self.spec_path, "r", encoding="utf-8") as f:
data = json.load(f)
return self._compute_hash(data)
@@ -240,12 +247,7 @@ class SpecManager:
# Patch Operations
# =========================================================================
def patch(
self,
path: str,
value: Any,
modified_by: str = "api"
) -> AtomizerSpec:
def patch(self, path: str, value: Any, modified_by: str = "api") -> AtomizerSpec:
"""
Apply a JSONPath-style modification.
@@ -306,7 +308,7 @@ class SpecManager:
"""Parse JSONPath into parts."""
# Handle both dot notation and bracket notation
parts = []
for part in re.split(r'\.|\[|\]', path):
for part in re.split(r"\.|\[|\]", path):
if part:
parts.append(part)
return parts
@@ -316,10 +318,7 @@ class SpecManager:
# =========================================================================
def add_node(
self,
node_type: str,
node_data: Dict[str, Any],
modified_by: str = "canvas"
self, node_type: str, node_data: Dict[str, Any], modified_by: str = "canvas"
) -> str:
"""
Add a new node (design var, extractor, objective, constraint).
@@ -353,20 +352,19 @@ class SpecManager:
self.save(data, modified_by)
# Broadcast node addition
self._broadcast({
"type": "node_added",
"node_type": node_type,
"node_id": node_id,
"modified_by": modified_by
})
self._broadcast(
{
"type": "node_added",
"node_type": node_type,
"node_id": node_id,
"modified_by": modified_by,
}
)
return node_id
def update_node(
self,
node_id: str,
updates: Dict[str, Any],
modified_by: str = "canvas"
self, node_id: str, updates: Dict[str, Any], modified_by: str = "canvas"
) -> None:
"""
Update an existing node.
@@ -396,11 +394,7 @@ class SpecManager:
self.save(data, modified_by)
def remove_node(
self,
node_id: str,
modified_by: str = "canvas"
) -> None:
def remove_node(self, node_id: str, modified_by: str = "canvas") -> None:
"""
Remove a node and all edges referencing it.
@@ -427,24 +421,18 @@ class SpecManager:
# Remove edges referencing this node
if "canvas" in data and data["canvas"] and "edges" in data["canvas"]:
data["canvas"]["edges"] = [
e for e in data["canvas"]["edges"]
e
for e in data["canvas"]["edges"]
if e.get("source") != node_id and e.get("target") != node_id
]
self.save(data, modified_by)
# Broadcast node removal
self._broadcast({
"type": "node_removed",
"node_id": node_id,
"modified_by": modified_by
})
self._broadcast({"type": "node_removed", "node_id": node_id, "modified_by": modified_by})
def update_node_position(
self,
node_id: str,
position: Dict[str, float],
modified_by: str = "canvas"
self, node_id: str, position: Dict[str, float], modified_by: str = "canvas"
) -> None:
"""
Update a node's canvas position.
@@ -456,12 +444,7 @@ class SpecManager:
"""
self.update_node(node_id, {"canvas_position": position}, modified_by)
def add_edge(
self,
source: str,
target: str,
modified_by: str = "canvas"
) -> None:
def add_edge(self, source: str, target: str, modified_by: str = "canvas") -> None:
"""
Add a canvas edge between nodes.
@@ -483,19 +466,11 @@ class SpecManager:
if edge.get("source") == source and edge.get("target") == target:
return # Already exists
data["canvas"]["edges"].append({
"source": source,
"target": target
})
data["canvas"]["edges"].append({"source": source, "target": target})
self.save(data, modified_by)
def remove_edge(
self,
source: str,
target: str,
modified_by: str = "canvas"
) -> None:
def remove_edge(self, source: str, target: str, modified_by: str = "canvas") -> None:
"""
Remove a canvas edge.
@@ -508,7 +483,8 @@ class SpecManager:
if "canvas" in data and data["canvas"] and "edges" in data["canvas"]:
data["canvas"]["edges"] = [
e for e in data["canvas"]["edges"]
e
for e in data["canvas"]["edges"]
if not (e.get("source") == source and e.get("target") == target)
]
@@ -524,7 +500,7 @@ class SpecManager:
code: str,
outputs: List[str],
description: Optional[str] = None,
modified_by: str = "claude"
modified_by: str = "claude",
) -> str:
"""
Add a custom extractor function.
@@ -546,9 +522,7 @@ class SpecManager:
try:
compile(code, f"<custom:{name}>", "exec")
except SyntaxError as e:
raise SpecValidationError(
f"Invalid Python syntax: {e.msg} at line {e.lineno}"
)
raise SpecValidationError(f"Invalid Python syntax: {e.msg} at line {e.lineno}")
data = self.load_raw()
@@ -561,13 +535,9 @@ class SpecManager:
"name": description or f"Custom: {name}",
"type": "custom_function",
"builtin": False,
"function": {
"name": name,
"module": "custom_extractors.dynamic",
"source_code": code
},
"function": {"name": name, "module": "custom_extractors.dynamic", "source_code": code},
"outputs": [{"name": o, "metric": "custom"} for o in outputs],
"canvas_position": self._auto_position("extractor", data)
"canvas_position": self._auto_position("extractor", data),
}
data["extractors"].append(extractor)
@@ -580,7 +550,7 @@ class SpecManager:
extractor_id: str,
code: Optional[str] = None,
outputs: Optional[List[str]] = None,
modified_by: str = "claude"
modified_by: str = "claude",
) -> None:
"""
Update an existing custom function.
@@ -611,9 +581,7 @@ class SpecManager:
try:
compile(code, f"<custom:{extractor_id}>", "exec")
except SyntaxError as e:
raise SpecValidationError(
f"Invalid Python syntax: {e.msg} at line {e.lineno}"
)
raise SpecValidationError(f"Invalid Python syntax: {e.msg} at line {e.lineno}")
if "function" not in extractor:
extractor["function"] = {}
extractor["function"]["source_code"] = code
@@ -672,7 +640,7 @@ class SpecManager:
"design_variable": "dv",
"extractor": "ext",
"objective": "obj",
"constraint": "con"
"constraint": "con",
}
prefix = prefix_map.get(node_type, node_type[:3])
@@ -697,7 +665,7 @@ class SpecManager:
"design_variable": "design_variables",
"extractor": "extractors",
"objective": "objectives",
"constraint": "constraints"
"constraint": "constraints",
}
return section_map.get(node_type, node_type + "s")
@@ -709,7 +677,7 @@ class SpecManager:
"design_variable": 50,
"extractor": 740,
"objective": 1020,
"constraint": 1020
"constraint": 1020,
}
x = x_positions.get(node_type, 400)
@@ -729,11 +697,123 @@ class SpecManager:
return {"x": x, "y": y}
# =========================================================================
# Intake Workflow Methods
# =========================================================================
def update_status(self, status: str, modified_by: str = "api") -> None:
"""
Update the spec status field.
Args:
status: New status (draft, introspected, configured, validated, ready, running, completed, failed)
modified_by: Who/what is making the change
"""
data = self.load_raw()
data["meta"]["status"] = status
self.save(data, modified_by)
def get_status(self) -> str:
"""
Get the current spec status.
Returns:
Current status string
"""
if not self.exists():
return "unknown"
data = self.load_raw()
return data.get("meta", {}).get("status", "draft")
def add_introspection(
self, introspection_data: Dict[str, Any], modified_by: str = "introspection"
) -> None:
"""
Add introspection data to the spec's model section.
Args:
introspection_data: Dict with timestamp, expressions, mass_kg, etc.
modified_by: Who/what is making the change
"""
data = self.load_raw()
if "model" not in data:
data["model"] = {}
data["model"]["introspection"] = introspection_data
data["meta"]["status"] = "introspected"
self.save(data, modified_by)
def add_baseline(
self, baseline_data: Dict[str, Any], modified_by: str = "baseline_solve"
) -> None:
"""
Add baseline solve results to introspection data.
Args:
baseline_data: Dict with timestamp, solve_time_seconds, mass_kg, etc.
modified_by: Who/what is making the change
"""
data = self.load_raw()
if "model" not in data:
data["model"] = {}
if "introspection" not in data["model"] or data["model"]["introspection"] is None:
data["model"]["introspection"] = {}
data["model"]["introspection"]["baseline"] = baseline_data
# Update status based on baseline success
if baseline_data.get("success", False):
data["meta"]["status"] = "validated"
self.save(data, modified_by)
def set_topic(self, topic: str, modified_by: str = "api") -> None:
"""
Set the spec's topic field.
Args:
topic: Topic folder name
modified_by: Who/what is making the change
"""
data = self.load_raw()
data["meta"]["topic"] = topic
self.save(data, modified_by)
def get_introspection(self) -> Optional[Dict[str, Any]]:
"""
Get introspection data from spec.
Returns:
Introspection dict or None if not present
"""
if not self.exists():
return None
data = self.load_raw()
return data.get("model", {}).get("introspection")
def get_design_candidates(self) -> List[Dict[str, Any]]:
"""
Get expressions marked as design variable candidates.
Returns:
List of expression dicts where is_candidate=True
"""
introspection = self.get_introspection()
if not introspection:
return []
expressions = introspection.get("expressions", [])
return [e for e in expressions if e.get("is_candidate", False)]
# =========================================================================
# Factory Function
# =========================================================================
def get_spec_manager(study_path: Union[str, Path]) -> SpecManager:
"""
Get a SpecManager instance for a study.