Update Cheminformatrics use Cases (#155)

* Update Cheminformatrics use Cases

Add _cheminfo_tools.py with lipinksi filter , View Mol Image , View mol filter with smarts and smiles and highlights are done .

* Delete binary files. Create "Cheminformatics" folder for examples.

* MACCSkeys was undefined. rows was unused.

* Give ops human-readable names.

* Example workspace without images.

* Collapse parameters on "image" type boxes.

* Allow slow visualization boxes too.

* Simpler gallery drawing.

* Output for visualizations is now left empty.

---------

Co-authored-by: Daniel Darabos <[email protected]>

examples/Image table.lynxkite.json

@@ -27,7 +27,7 @@
     {
       "data": {
         "__execution_delay": null,
-        "collapsed": true,
+        "collapsed": false,
         "display": null,
         "error": null,
         "input_metadata": [],
@@ -55,8 +55,8 @@
       "height": 200.0,
       "id": "Example image table 1",
       "position": {
-        "x": 213.60043945845376,
-        "y": 306.98088700969373
+        "x": 356.1935187064265,
+        "y": 224.8472733628614
       },
       "type": "basic",
       "width": 280.0
@@ -138,8 +138,8 @@
       "height": 440.0,
       "id": "View tables 1",
       "position": {
-        "x": 626.2831607914023,
-        "y": 109.55448939208392
+        "x": 757.4687936995374,
+        "y": 116.39895719598661
       },
       "type": "table_view",
       "width": 376.0
@@ -198,14 +198,14 @@
         "title": "Import CSV"
       },
       "dragHandle": ".bg-primary",
-      "height": 313.0,
+      "height": 339.0,
       "id": "Import CSV 1",
       "position": {
         "x": 13.802068621055497,
         "y": -269.65065144888104
       },
       "type": "basic",
-      "width": 216.0
+      "width": 296.0
     },
     {
       "data": {
@@ -282,15 +282,15 @@
         "params": {
           "limit": 100.0
         },
-        "status": "done",
+        "status": "planned",
         "title": "View tables"
       },
       "dragHandle": ".bg-primary",
       "height": 418.0,
       "id": "View tables 2",
       "position": {
-        "x": 548.7706661684929,
-        "y": -316.9626796191875
+        "x": 815.4121289519509,
+        "y": -330.8232285057863
       },
       "type": "table_view",
       "width": 1116.0
@@ -300,7 +300,7 @@
         "__execution_delay": 0.0,
         "collapsed": null,
         "display": null,
-        "error": null,
+        "error": "module 'rdkit.Chem' has no attribute 'Draw'",
         "input_metadata": [
           {}
         ],
@@ -354,8 +354,8 @@
       "height": 296.0,
       "id": "Draw molecules 1",
       "position": {
-        "x": 289.42386787591244,
-        "y": -258.0823121715324
+        "x": 351.1956913898301,
+        "y": -235.00831568554486
       },
       "type": "basic",
       "width": 212.0

lynxkite-app/web/src/workspace/nodes/NodeWithImage.tsx

@@ -3,7 +3,7 @@ import { NodeWithParams } from "./NodeWithParams";
 
 const NodeWithImage = (props: any) => {
   return (
-    <NodeWithParams {...props}>
+    <NodeWithParams collapsed {...props}>
       {props.data.display && <img src={props.data.display} alt="Node Display" />}
     </NodeWithParams>
   );

lynxkite-core/src/lynxkite/core/ops.py

@@ -129,7 +129,7 @@ class Result:
     `input_metadata` is a list of JSON objects describing each input.
     """
 
-    output: typing.Any = None
+    output: typing.Any | None = None
     display: ReadOnlyJSON | None = None
     error: str | None = None
     input_metadata: ReadOnlyJSON | None = None
@@ -187,7 +187,6 @@ class Op(BaseConfig):
         res = self.func(*inputs, **params)
         if not isinstance(res, Result):
             # Automatically wrap the result in a Result object, if it isn't already.
-            res = Result(output=res)
             if self.type in [
                 "visualization",
                 "table_view",
@@ -195,9 +194,10 @@ class Op(BaseConfig):
                 "image",
                 "molecule",
             ]:
-                # If the operation is some kind of visualization, we use the output as the
-                # value to display by default.
-                res.display = res.output
+                # If the operation is a visualization, we use the returned value for display.
+                res = Result(display=res)
+            else:
+                res = Result(output=res)
         return res
 
     def get_input(self, name: str):
@@ -237,6 +237,10 @@ def op(
 
     def decorator(func):
         sig = inspect.signature(func)
+        _view = view
+        if view == "matplotlib":
+            _view = "image"
+            func = matplotlib_to_image(func)
         if slow:
             func = mem.cache(func)
             func = _global_slow(func)
@@ -256,10 +260,6 @@ def op(
             _outputs = [Output(name=name, type=None) for name in outputs]
         else:
             _outputs = [Output(name="output", type=None)] if view == "basic" else []
-        _view = view
-        if view == "matplotlib":
-            _view = "image"
-            func = matplotlib_to_image(func)
         op = Op(
             func=func,
             name=name,

lynxkite-core/src/lynxkite/core/workspace.py

@@ -65,10 +65,14 @@ class WorkspaceNode(BaseConfig):
         self.data.status = NodeStatus.done
         if hasattr(self, "_crdt"):
             with self._crdt.doc.transaction():
-                self._crdt["data"]["display"] = self.data.display
-                self._crdt["data"]["input_metadata"] = self.data.input_metadata
-                self._crdt["data"]["error"] = self.data.error
-                self._crdt["data"]["status"] = NodeStatus.done
+                try:
+                    self._crdt["data"]["status"] = NodeStatus.done
+                    self._crdt["data"]["display"] = self.data.display
+                    self._crdt["data"]["input_metadata"] = self.data.input_metadata
+                    self._crdt["data"]["error"] = self.data.error
+                except Exception as e:
+                    self._crdt["data"]["error"] = str(e)
+                    raise e
 
     def publish_error(self, error: Exception | str | None):
         """Can be called with None to clear the error state."""
@@ -176,7 +180,6 @@ class Workspace(BaseConfig):
                     # If the node is connected to a CRDT, update that too.
                     if hasattr(node, "_crdt"):
                         node._crdt["data"]["meta"] = op.model_dump()
-                        print("set metadata to", op)
                 if node.type != op.type:
                     node.type = op.type
                     if hasattr(node, "_crdt"):

lynxkite-core/tests/test_ops.py

@@ -104,4 +104,4 @@ def test_visualization_operations_display_is_populated_automatically():
 
     result = ops.CATALOGS["test"]["display_op"]()
     assert isinstance(result, ops.Result)
-    assert result.output == result.display == {"display_value": 1}
+    assert result.display == {"display_value": 1}

lynxkite-graph-analytics/src/lynxkite_graph_analytics/core.py

@@ -222,6 +222,7 @@ async def _execute_node(node, ws, catalog, outputs):
     try:
         result = op(*inputs, **params)
         result.output = await await_if_needed(result.output)
+        result.display = await await_if_needed(result.display)
     except Exception as e:
         if not os.environ.get("LYNXKITE_SUPPRESS_OP_ERRORS"):
             traceback.print_exc()