Merge pull request #61 from brianpos/BP-2025-07-BugFixesAndEnhancements

Bug fixes and enhancements

Author: ruscoder

.gitattributes

@@ -0,0 +1,30 @@
+# Set default behavior to automatically normalize line endings
+* text=auto
+
+# Force specific files to have Unix line endings (LF)
+*.py text eol=lf
+*.md text eol=lf
+*.yml text eol=lf
+*.yaml text eol=lf
+*.toml text eol=lf
+*.ini text eol=lf
+*.txt text eol=lf
+*.json text eol=lf
+
+# Ensure these files are always treated as text and use LF
+Dockerfile text eol=lf
+*.dockerfile text eol=lf
+
+# Declare files that will always have CRLF line endings on checkout
+*.bat text eol=crlf
+
+# Denote all files that are truly binary and should not be modified
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.gif binary
+*.ico binary
+*.pdf binary
+*.zip binary
+*.tar.gz binary
+*.whl binary

fhirpathpy/__init__.py

@@ -35,11 +35,31 @@ def apply_parsed_path(resource, parsedPath, context=None, model=None, options=No
             (options or {}).get("userInvocationTable", {})
         ),
     }
+    
+    # Add trace callback if provided in options
+    if options and "traceFn" in options:
+        ctx["traceFn"] = options["traceFn"]
+    
     node = do_eval(ctx, dataRoot, parsedPath["children"][0])
 
     # Resolve any internal "ResourceNode" instances.  Continue to let FP_Type
     # subclasses through.
 
+    if options and options.get("returnRawData", False):
+        if isinstance(node, list):
+            res = []
+            # Filter out intenal representation of primitive extensions
+            # even in this raw data mode (as they are not a part of the output)
+            for item in node:
+                if isinstance(item, ResourceNode):
+                    if isinstance(item.data, dict):
+                        keys = list(item.data.keys())
+                        if keys == ["extension"]:
+                            continue
+                res.append(item)
+            return res
+        return node
+    
     def visit(node):
         data = get_data(node)
 

fhirpathpy/engine/__init__.py

@@ -83,10 +83,11 @@ def doInvoke(ctx, fn_name, data, raw_params):
     params = []
     argTypes = invocation["arity"][paramsNumber]
 
+    thisValue = ctx["$this"] if "$this" in ctx else ctx["dataRoot"]
     for i in range(0, paramsNumber):
         tp = argTypes[i]
         pr = raw_params[i]
-        params.append(make_param(ctx, data, tp, pr))
+        params.append(make_param(ctx, thisValue, tp, pr))
 
     params.insert(0, data)
     params.insert(0, ctx)

fhirpathpy/engine/evaluators/__init__.py

@@ -174,6 +174,8 @@ def create_reduce_member_invocation(model, key):
     def func(acc, res):
         res = nodes.ResourceNode.create_node(res)
         childPath = f"{res.path}.{key}" if res.path else f"_.{key}"
+        fullPath = f"{res.propName}.{key}" if res.propName else childPath # The full path to the node (weill evenutally be) e.g. Patient.name[0].given
+        fullPath = fullPath.replace("_", "")
 
         actualTypes = None
         toAdd = None
@@ -212,16 +214,16 @@ def func(acc, res):
 
         if util.is_some(toAdd):
             if isinstance(toAdd, list):
-                mapped = [nodes.ResourceNode.create_node(x, childPath) for x in toAdd]
+                mapped = [nodes.ResourceNode.create_node(x, childPath, propName=f"{fullPath}[{i}]", index=i) for i, x in enumerate(toAdd)]
                 acc = acc + mapped
             else:
-                acc.append(nodes.ResourceNode.create_node(toAdd, childPath))
+                acc.append(nodes.ResourceNode.create_node(toAdd, childPath, propName=fullPath))
         if util.is_some(toAdd_):
             if isinstance(toAdd_, list):
-                mapped = [nodes.ResourceNode.create_node(x, childPath) for x in toAdd_]
+                mapped = [nodes.ResourceNode.create_node(x, childPath, propName=f"{fullPath}[{i}]", index=i) for i, x in enumerate(toAdd_)]
                 acc = acc + mapped
             else:
-                acc.append(nodes.ResourceNode.create_node(toAdd_, childPath))
+                acc.append(nodes.ResourceNode.create_node(toAdd_, childPath, propName=fullPath))
         return acc
 
     return func

fhirpathpy/engine/invocations/misc.py

@@ -21,7 +21,12 @@ def iif_macro(ctx, data, cond, ok, fail=None):
 
 
 def trace_fn(ctx, x, label=""):
-    print("TRACE:[" + label + "]", str(x))
+    # Check if a custom trace callback is provided in the context
+    if "traceFn" in ctx and callable(ctx["traceFn"]):
+        ctx["traceFn"](label, x)
+    else:
+        # Fall back to console output if no callback is provided
+        print("TRACE:[" + label + "]", str(x))
     return x
 
 

fhirpathpy/engine/invocations/navigation.py

@@ -6,7 +6,7 @@
 create_node = nodes.ResourceNode.create_node
 
 
-def create_reduce_children(ctx):
+def create_reduce_children(ctx, exclude_primitive_extensions):
     model = ctx["model"]
 
     def func(acc, res):
@@ -21,35 +21,61 @@ def func(acc, res):
                 value = data[prop]
                 childPath = ""
 
+                # extensions shouldn't filter through here, yet they should for descendants?
+                # unless this item is the node that is being processed (primitive extension)
+                # though if you filter it, descendants will not work too
+                if prop.startswith("_") and exclude_primitive_extensions:
+                    continue
+
                 if res.path is not None:
                     childPath = res.path + "." + prop
 
+                fullPath = f"{res.propName}.{prop}" if res.propName else childPath # The full path to the node (weill evenutally be) e.g. Patient.name[0].given
+                fullPath = fullPath.replace("_", "")
+
+                if prop == "extension":
+                    childPath = "Extension"
+
                 if (
                     isinstance(model, dict)
                     and "pathsDefinedElsewhere" in model
                     and childPath in model["pathsDefinedElsewhere"]
                 ):
                     childPath = model["pathsDefinedElsewhere"][childPath]
 
+                childPath = (
+                    model["path2Type"].get(childPath, childPath)
+                    if isinstance(model, dict) and "path2Type" in model
+                    else childPath
+                )
+
+                # If the prop tolower ends with the type tolower
+                if prop.lower().endswith(childPath.lower()) and len(prop) > len(childPath):
+                    # Check if the path is actually in the choice types
+                    altPropName = res.path + "." + prop[:-len(childPath)]
+                    actualTypes = model["choiceTypePaths"].get(altPropName, [])
+                    if len(actualTypes) > 0:
+                        # If it is, we can use it
+                        fullPath = f"{res.propName}.{prop[:-len(childPath)]}"
+
                 if isinstance(value, list):
-                    mapped = [create_node(n, childPath) for n in value]
+                    mapped = [create_node(n, childPath, propName=f"{fullPath}[{i}]", index=i) for i, n in enumerate(value)]
                     acc = acc + mapped
                 else:
-                    acc.append(create_node(value, childPath))
+                    acc.append(create_node(value, childPath, propName=fullPath))
         return acc
 
     return func
 
 
 def children(ctx, coll):
-    return reduce(create_reduce_children(ctx), coll, [])
+    return reduce(create_reduce_children(ctx, True), coll, [])
 
 
 def descendants(ctx, coll):
     res = []
-    ch = children(ctx, coll)
+    ch = reduce(create_reduce_children(ctx, False), coll, [])
     while len(ch) > 0:
         res = res + ch
-        ch = children(ctx, ch)
-
+        ch = reduce(create_reduce_children(ctx, False), ch, [])
     return res

fhirpathpy/engine/nodes.py

@@ -8,6 +8,7 @@
 import json
 import re
 import time
+from typing import Optional
 
 
 timeRE = (
@@ -821,7 +822,7 @@ class ResourceNode:
     * @param _data additional data stored in a property named with "_" prepended.
     """
 
-    def __init__(self, data, path, _data=None):
+    def __init__(self, data, path, _data=None, propName=None, index=None):
         """
         If data is a resource (maybe a contained resource) reset the path
         information to the resource type.
@@ -832,6 +833,8 @@ def __init__(self, data, path, _data=None):
         self.path = path
         self.data = data
         self._data = _data
+        self.propName: Optional[str] = propName
+        self.index: Optional[int] = index
 
     def __eq__(self, value):
         if isinstance(value, ResourceNode):
@@ -864,10 +867,10 @@ def toJSON(self):
         return json.dumps(self.data)
 
     @staticmethod
-    def create_node(data, path=None, _data=None):
+    def create_node(data, path=None, _data=None, propName=None, index=None):
         if isinstance(data, ResourceNode):
             return data
-        return ResourceNode(data, path, _data)
+        return ResourceNode(data, path, _data, propName, index)
 
     def convert_data(self):
         data = self.data

tests/test_evaluators.py

@@ -193,7 +193,7 @@ def existence_functions_test(resource, path, expected):
     ("resource", "path", "expected"),
     [
         ({}, "iif(true, 'a', 'b')", ["a"]),
-        ({"a": {"b": [1, 2, 3]}}, "a.b.trace()", [1, 2, 3]),
+        ({"a": {"b": [1, 2, 3]}}, "a.b.trace('t')", [1, 2, 3]),
         ({"a": True}, "a.toInteger()", [1]),
         ({"a": False}, "a.toInteger()", [0]),
         ({"a": True}, "a.toDecimal()", [1.0]),