tooluniverse 0.2.0__py3-none-any.whl → 1.0.1__py3-none-any.whl

tooluniverse/openfda_adv_tool.py

@@ -0,0 +1,283 @@
+import os
+import copy
+import requests
+import urllib.parse
+from .base_tool import BaseTool
+from .tool_registry import register_tool
+
+# ---- Helper: human readable -> openFDA code mapping ----
+HUMAN_TO_FDA_MAP = {
+    "fulfillexpeditecriteria": {"Yes": "1", "No": "2"},
+    "patient.patientsex": {"Unknown": "0", "Male": "1", "Female": "2"},
+    "patient.patientagegroup": {
+        "Neonate": "1",
+        "Infant": "2",
+        "Child": "3",
+        "Adolescent": "4",
+        "Adult": "5",
+        "Elderly": "6",
+    },
+    "patientonsetageunit": {
+        "Decade": "800",
+        "Year": "801",
+        "Month": "802",
+        "Week": "803",
+        "Day": "804",
+        "Hour": "805",
+    },
+    "patient.reaction.reactionoutcome": {
+        "Recovered/resolved": "1",
+        "Recovering/resolving": "2",
+        "Not recovered/not resolved": "3",
+        "Recovered/resolved with sequelae": "4",
+        "Fatal": "5",
+        "Unknown": "6",
+    },
+    "serious": {"Yes": "1", "No": "2"},
+    "seriousnessdeath": {"Yes": "1"},
+    "seriousnesshospitalization": {"Yes": "1"},
+    "seriousnessdisabling": {"Yes": "1"},
+    "seriousnesslifethreatening": {"Yes": "1"},
+    "seriousnessother": {"Yes": "1"},
+    "primarysource.qualification": {
+        "Physician": "1",
+        "Pharmacist": "2",
+        "Other health professional": "3",
+        "Lawyer": "4",
+        "Consumer or non-health professional": "5",
+    },
+    "patient.drug.drugcharacterization": {
+        "Suspect": "1",
+        "Concomitant": "2",
+        "Interacting": "3",
+    },
+    "patient.drug.drugadministrationroute": {
+        "Oral": "048",
+        "Intravenous": "042",
+        "Intramuscular": "030",
+        "Subcutaneous": "058",
+        "Rectal": "054",
+        "Topical": "061",
+        "Respiratory (inhalation)": "055",
+        "Ophthalmic": "047",
+        "Unknown": "065",
+    },
+}
+
+
+# ---- Base Tool Class ----
+@register_tool("FDADrugAdverseEventTool")
+class FDADrugAdverseEventTool(BaseTool):
+    def __init__(
+        self,
+        tool_config,
+        endpoint_url="https://api.fda.gov/drug/event.json",
+        api_key=None,
+    ):
+        super().__init__(tool_config)
+        self.endpoint_url = endpoint_url
+        self.api_key = api_key or os.getenv("FDA_API_KEY")
+        self.search_fields = tool_config.get("fields", {}).get("search_fields", {})
+        self.return_fields = tool_config.get("fields", {}).get("return_fields", [])
+        self.count_field = tool_config.get("count_field") or (
+            self.return_fields[0] if self.return_fields else None
+        )
+        self.return_fields_mapping = tool_config.get("fields", {}).get(
+            "return_fields_mapping", {}
+        )
+
+        if not self.count_field:
+            raise ValueError(
+                "Either 'count_field' or 'return_fields' must be defined in tool_config."
+            )
+
+        # Store allowed enum values
+        self.parameter_enums = {}
+        if "parameter" in tool_config and "properties" in tool_config["parameter"]:
+            for param_name, param_def in tool_config["parameter"]["properties"].items():
+                if "enum" in param_def:
+                    self.parameter_enums[param_name] = param_def["enum"]
+
+    def run(self, arguments):
+        arguments = copy.deepcopy(arguments)
+
+        # Validate enum parameters
+        validation_error = self.validate_enum_arguments(arguments)
+        if validation_error:
+            return {"error": validation_error}
+
+        response = self._search(arguments)
+        return self._post_process(response)
+
+    def validate_enum_arguments(self, arguments):
+        """Validate that enum-based arguments match the allowed values"""
+        for param_name, value in arguments.items():
+            if param_name in self.parameter_enums and value is not None:
+                allowed_values = self.parameter_enums[param_name]
+                if value not in allowed_values:
+                    return f"Invalid value '{value}' for parameter '{param_name}'. Allowed values are: {', '.join(allowed_values)}"
+        return None
+
+    def _post_process(self, response):
+        if not response or not isinstance(response, list):
+            return []
+
+        if not self.return_fields_mapping:
+            return response
+
+        mapped_results = []
+        for item in response:
+            try:
+                term = item.get("term")
+                count = item.get("count", 0)
+                mapped_term = self.return_fields_mapping.get(self.count_field, {}).get(
+                    str(term), term
+                )
+                mapped_results.append({"term": mapped_term, "count": count})
+            except Exception:
+                # Keep the original term in case of an exception
+                mapped_results.append(item)
+
+        return mapped_results
+
+    def _search(self, arguments):
+        search_parts = []
+        for param_name, value in arguments.items():
+            fda_fields = self.search_fields.get(
+                param_name, [param_name]
+            )  # Map param -> FDA field
+
+            # Apply value mapping if needed
+            mapping_error, mapped_value = self._map_value(param_name, value)
+            if mapping_error:
+                return [{"error": mapping_error}]
+            if mapped_value is None:
+                continue  # Skip this field if instructed
+
+            # Build search parts
+            for fda_field in fda_fields:
+                if isinstance(mapped_value, str) and " " in mapped_value:
+                    search_parts.append(f'{fda_field}:"{mapped_value}"')
+                else:
+                    search_parts.append(f"{fda_field}:{mapped_value}")
+
+        # Final search query
+        search_query = "+AND+".join(search_parts)
+        search_encoded = urllib.parse.quote(search_query, safe='+:"')
+
+        # Build URL
+        if self.api_key:
+            url = f"{self.endpoint_url}?api_key={self.api_key}&search={search_encoded}&count={self.count_field}"
+        else:
+            url = (
+                f"{self.endpoint_url}?search={search_encoded}&count={self.count_field}"
+            )
+
+        # API request
+        try:
+            response = requests.get(url)
+            response.raise_for_status()
+            response = response.json()
+            if "results" in response:
+                response = response["results"]
+            return response
+        except requests.exceptions.RequestException as e:
+            return [{"error": f"API request failed: {str(e)}"}]
+
+    def _map_value(self, param_name, value):
+        # Special handling for seriousness fields: if value is "No", skip this field
+        seriousness_fields = {
+            "seriousnessdeath",
+            "seriousnesshospitalization",
+            "seriousnessdisabling",
+            "seriousnesslifethreatening",
+            "seriousnessother",
+        }
+        if param_name in seriousness_fields:
+            if value == "No":
+                return None, None  # Signal to skip this field
+            if value == "Yes":
+                return None, "1"
+            # If not Yes/No, error
+            return (
+                f"Invalid value '{value}' for '{param_name}'. Allowed values: ['Yes', 'No']",
+                None,
+            )
+
+        if param_name in HUMAN_TO_FDA_MAP:
+            value_map = HUMAN_TO_FDA_MAP[param_name]
+            if value not in value_map:
+                print("No mapping found for value:", value, "skipping")
+                allowed_values = list(value_map.keys())
+                return (
+                    f"Invalid value '{value}' for '{param_name}'. Allowed values: {allowed_values}",
+                    None,
+                )
+            return None, value_map[value]
+        return None, value
+
+
+@register_tool("FDACountAdditiveReactionsTool")
+class FDACountAdditiveReactionsTool(FDADrugAdverseEventTool):
+    """
+    Leverage openFDA API to count adverse reaction events across multiple drugs in one request.
+    """
+
+    def __init__(
+        self,
+        tool_config,
+        endpoint_url="https://api.fda.gov/drug/event.json",
+        api_key=None,
+    ):
+        super().__init__(tool_config)
+
+    def run(self, arguments):
+        # Make a copy to avoid modifying the original
+        arguments = copy.deepcopy(arguments)
+
+        # Validate medicinalproducts list first
+        drugs = arguments.pop("medicinalproducts", [])
+        if not drugs:
+            return {"error": "`medicinalproducts` list is required."}
+        if not isinstance(drugs, list):
+            return {"error": "`medicinalproducts` must be a list of drug names."}
+
+        # Validate the remaining enum parameters
+        validation_error = self.validate_enum_arguments(arguments)
+        if validation_error:
+            return {"error": validation_error}
+
+        # Build OR clause for multiple drugs
+        escaped = []
+        for d in drugs:
+            val = urllib.parse.quote(d, safe="")
+            escaped.append(f"patient.drug.medicinalproduct:{val}")
+        or_clause = "+OR+".join(escaped)
+
+        # Combine additional filters
+        filters = []
+        for k, v in arguments.items():
+            mapping_error, mapped = self._map_value(k, v)
+            if mapping_error:
+                return {"error": mapping_error}
+            if mapped is None:
+                continue  # Skip this field if instructed
+            filters.append(f"{k}:{mapped}")
+
+        filter_str = "+AND+".join(filters) if filters else ""
+        search_query = f"({or_clause})" + (f"+AND+{filter_str}" if filter_str else "")
+
+        # Call API
+        if self.api_key:
+            url = f"{self.endpoint_url}?api_key={self.api_key}&search={search_query}&count={self.count_field}"
+        else:
+            url = f"{self.endpoint_url}?search={search_query}&count={self.count_field}"
+
+        try:
+            resp = requests.get(url)
+            resp.raise_for_status()
+            results = resp.json().get("results", [])
+            results = self._post_process(results)
+            return results
+        except requests.exceptions.RequestException as e:
+            return {"error": f"API request failed: {str(e)}"}