tooluniverse 0.2.0__py3-none-any.whl → 1.0.0__py3-none-any.whl

tooluniverse/ctg_tool.py

@@ -0,0 +1,1002 @@
+from copy import deepcopy
+from urllib.parse import urljoin
+from .restful_tool import RESTfulTool, execute_RESTful_query
+from .tool_registry import register_tool
+
+
+@register_tool("ClinicalTrialsTool")
+class ClinicalTrialsTool(RESTfulTool):
+    def __init__(self, tool_config):
+        base_url = "https://clinicaltrials.gov/api/v2"  # Base URL for CTG API v2
+        full_url = urljoin(base_url + "/", tool_config["tool_url"].lstrip("/"))
+        super().__init__(tool_config, full_url)
+
+        self.list_params_to_join = [
+            "filter.ids",
+            "filter.overallStatus",
+            "fields",
+            "sort",
+        ]
+
+        self.param_name_mapper = {
+            "condition": "query.cond",
+            "title": "query.titles",
+            "intervention": "query.intr",
+            "outcome": "query.outc",
+            "overall_status": "filter.overallStatus",
+            "query_term": "query.term",
+        }
+
+    def _map_param_names(self, arguments):
+        """
+        Maps the parameter names in the arguments dictionary to the expected parameter names defined in the tool's JSON configuration.
+
+        Args:
+            arguments (dict): Runtime arguments provided to the tool's run method.
+
+        Returns:
+            dict: A new dictionary with mapped parameter names.
+        """
+
+        mapped_arguments = {}
+        for key, value in arguments.items():
+            if key in self.param_name_mapper:
+                mapped_key = self.param_name_mapper[key]
+                mapped_arguments[mapped_key] = value
+            else:
+                mapped_arguments[key] = value
+        return mapped_arguments
+
+    def _prepare_api_params(self, arguments):
+        """
+        Prepares the dictionary of parameters for the API query string based on tool config and runtime arguments.
+
+        Args:
+            arguments (dict): Runtime arguments provided to the tool's run method.
+
+        Returns:
+            dict: A dictionary of parameters ready for the API requests.
+        """
+        api_params = {}
+
+        for param_name, value in arguments.items():
+            if value is not None:
+                # Handle parameters defined as lists that need joining
+                if param_name in self.list_params_to_join and isinstance(value, list):
+                    # Join list items into a comma-separated string
+                    api_params[param_name] = ",".join(map(str, value))
+                else:
+                    api_params[param_name] = value
+
+        return api_params
+
+    def _format_endpoint_url(self, arguments):
+        """
+        Formats the endpoint URL by substituting path parameters (like {nctId}) with values from the arguments dictionary.
+
+        Args:
+            arguments (dict): Runtime arguments provided to the tool's run method.
+
+        Returns:
+            str: The formatted endpoint URL.
+        """
+        url_to_format = self.endpoint_url
+        try:
+            # Find keys in arguments that match placeholders in the URL template
+            # e.g., if url_to_format is ".../studies/{nctId}", find 'nctId' in arguments
+            path_params = {
+                k: v for k, v in arguments.items() if f"{{{k}}}" in url_to_format
+            }
+            # Perform the substitution
+            return url_to_format.format(**path_params)
+        except KeyError as e:
+            # This might happen if a placeholder exists but the corresponding key is missing in arguments
+            print(
+                f"Warning: Missing key {e} in arguments for URL formatting: {url_to_format}"
+            )
+            # Return the original URL; the API call will likely fail, but avoids crashing here
+            return url_to_format
+
+    def run(self, arguments):
+        raise NotImplementedError("The run method should be implemented in subclasses.")
+
+
+@register_tool("ClinicalTrialsSearchTool")
+# Searching studies (/studies)
+class ClinicalTrialsSearchTool(ClinicalTrialsTool):
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.default_params_not_shown = {
+            "format": "json",  # Default format for the response
+            "sort": "@relevance",  # Default sort order
+            "fields": [
+                "NCTId",
+                "BriefTitle",
+                # "OfficialTitle",
+                "OverallStatus",
+                # "StartDate",
+                # "PrimaryCompletionDate",
+                # "PrimaryOutcomeMeasure",
+                # "DescriptionModule",
+                "BriefSummary",
+                "Condition",
+                "Phase",
+                # "Intervention",
+                # "InterventionName",
+                # "InterventionArmGroupLabel",
+                # "InterventionOtherName",
+                # "WhyStopped",
+                # "HasResults",
+            ],  # NOTE: Can change this one
+            "countTotal": True,  # NOTE: Can change this one
+            "filter.advanced": "AREA[HasResults]true AND (AREA[Phase]PHASE2 OR AREA[Phase]PHASE3 OR AREA[Phase]PHASE4)",
+            # TODO: Consider adding a YEAR filter for the query to remove trials that are too early? E.g., "AREA[LastUpdatePostDate]RANGE[2000-01-01,MAX]"
+        }
+        # "title": {
+        #             "type": "string",
+        #             "description": "Query for study titles using Essie expression syntax (e.g., 'lung cancer').",
+        #             "required": false
+        #         },
+        # "outcome": {
+        #             "type": "string",
+        #             "description": "Query for outcome measures using Essie expression syntax (e.g., 'overall survival', 'adverse events', 'progress-free survival').",
+        #             "required": false
+        #         },
+        # "query.locn": {
+        #     "type": "string",
+        #     "description": "Query for location terms using Essie expression syntax (e.g., 'California')."
+        # },
+        # "overall_status": {
+        #             "type": "array",
+        #             "description": "Filter by a list of overall study statuses (e.g., ['RECRUITING', 'COMPLETED']). ",
+        #             "items": {
+        #                 "type": "string",
+        #                 "enum": ["ACTIVE_NOT_RECRUITING", "COMPLETED", "ENROLLING_BY_INVITATION", "NOT_YET_RECRUITING", "RECRUITING", "SUSPENDED", "TERMINATED", "WITHDRAWN", "AVAILABLE", "NO_LONGER_AVAILABLE", "TEMPORARILY_NOT_AVAILABLE", "APPROVED_FOR_MARKETING", "WITHHELD", "UNKNOWN"]
+        #             },
+        #             "required": false
+        #         },
+        # "filter.ids": {
+        #     "type": "array",
+        #     "description": "Filter by a list of NCT IDs (e.g., ['NCT04852770', 'NCT01728545']).",
+        #     "items": {
+        #         "type": "string"
+        #     }
+        # },
+        # "sort": {
+        #     "type": "array",
+        #     "description": "Comma- or pipe-separated list of fields to sort by for the studies, with optional direction. The returning studies are not sorted by default. Every list item contains a field/piece name and an optional sort direction (asc for ascending or desc for descending) after colon character (e.g., ['LastUpdatePostDate:desc', 'EnrollmentCount'], [@relevance]). Default sort order varies by field type. Special value '@relevance' sorts by query relevance.",
+        #     "items": {
+        #         "type": "string"
+        #     }
+        # },
+        # "fields": {
+        #     "type": "array",
+        #     "description": "List of fields to return (e.g., ['NCTId', 'BriefTitle', 'OverallStatus', 'Phase', 'PrimaryCompletionDate', 'PrimaryOutcomeMeasure']). By default, we look at the following fields: ['NCTId', 'BriefTitle', 'OfficialTitle', 'OverallStatus', 'StartDate', 'PrimaryCompletionDate', 'PrimaryOutcomeMeasure', 'DescriptionModule', 'Condition', 'Phase', 'WhyStopped', 'HasResults'].",
+        #     "items": {
+        #         "type": "string"
+        #     },
+        #     "required": false
+        # },
+
+    def run(self, arguments):
+        """
+        Executes the search query for clinical trials.
+
+        Args:
+            arguments (dict): A dictionary containing parameters provided by the user/LLM
+
+        Returns:
+            dict or str: The JSON response from the API as a dictionary,
+                         or raw text for non-JSON responses, or an error dictionary.
+        """
+        arguments = self._map_param_names(arguments)
+        query_params = deepcopy(self.query_schema)
+        expected_param_names = self._map_param_names(
+            self.parameters
+        ).keys()  # NOTE: Workaround for not having an aligned schema in the JSON config
+
+        # Prepare API parameters from arguments
+        for k in expected_param_names:
+            if k in arguments and arguments[k] is not None:
+                query_params[k] = arguments[k]
+
+        # Add default parameters that are not shown in the schema
+        for k, v in self.default_params_not_shown.items():
+            if k not in query_params:
+                query_params[k] = v
+
+        # Process list parameters that need to be joined
+        api_params = self._prepare_api_params(query_params)
+
+        # Fix a bug where 'countTotal' is a boolean but should be a string as input to API
+        if "countTotal" in api_params and isinstance(api_params["countTotal"], bool):
+            api_params["countTotal"] = str(api_params["countTotal"]).lower()
+
+        formatted_endpoint_url = self.endpoint_url
+
+        response = execute_RESTful_query(
+            endpoint_url=formatted_endpoint_url, variables=api_params
+        )
+
+        # Simplify the output if the response is valid
+        if (
+            response is not None
+            and response
+            and "studies" in response.keys()
+            and len(response["studies"]) > 0
+        ):
+            response = self._simplify_output(response)
+        else:
+            return "No studies found for the given query parameters. Please examine your input and try different parameters."
+
+        return response
+
+    def _simplify_output(self, response):
+        new_response = []
+
+        for study in response["studies"]:
+            new_study = {
+                "NCT ID": study["protocolSection"]["identificationModule"].get("nctId"),
+            }
+            if "identificationModule" in study["protocolSection"]:
+                new_study["brief_title"] = study["protocolSection"][
+                    "identificationModule"
+                ].get("briefTitle")
+            if "descriptionModule" in study["protocolSection"]:
+                new_study["brief_summary"] = study["protocolSection"][
+                    "descriptionModule"
+                ].get("briefSummary")
+            if "statusModule" in study["protocolSection"]:
+                new_study["overall_status"] = study["protocolSection"][
+                    "statusModule"
+                ].get("overallStatus")
+            if "conditionsModule" in study["protocolSection"]:
+                new_study["condition"] = study["protocolSection"][
+                    "conditionsModule"
+                ].get("conditions")
+            if "designModule" in study["protocolSection"]:
+                new_study["phase"] = study["protocolSection"]["designModule"].get(
+                    "phases"
+                )
+            new_study = {
+                k: v for k, v in new_study.items() if v is not None
+            }  # Remove None values
+            new_response.append(new_study)
+
+        # def remove_empty_values(obj):
+        #     if isinstance(obj, dict):
+        #         return {k: remove_empty_values(v) for k, v in obj.items()
+        #                 if v not in [0, [], None]}
+        #     elif isinstance(obj, list):
+        #         return [remove_empty_values(v) for v in obj if v not in [0, [], None]]
+        #     else:
+        #         return obj
+        # new_response = remove_empty_values(new_response)
+
+        new_response = {"studies": new_response}
+        if "nextPageToken" in response:
+            new_response["nextPageToken"] = response["nextPageToken"]
+        if "totalCount" in response:
+            new_response["total_count"] = response["totalCount"]
+
+        return new_response
+
+
+@register_tool("ClinicalTrialsDetailsTool")
+class ClinicalTrialsDetailsTool(ClinicalTrialsTool):
+    def __init__(self, tool_config):
+        super().__init__(tool_config)
+        self.default_params_not_shown = {
+            "format": "json",
+        }
+
+    def run(self, arguments):
+        arguments = self._map_param_names(arguments)
+        expected_param_names = self._map_param_names(self.parameters).keys()
+        query_params = deepcopy(self.query_schema)
+
+        nct_ids_list = arguments.get("nct_ids")
+        if (
+            not nct_ids_list
+            or not isinstance(nct_ids_list, list)
+            or len(nct_ids_list) == 0
+        ):
+            return {
+                "error": "Missing or invalid required parameter: nct_ids (must be a non-empty list)"
+            }
+        del arguments[
+            "nct_ids"
+        ]  # Remove 'nct_ids' from query_params as it is not a valid API parameter
+
+        # Prepare API parameters from arguments
+        for k in expected_param_names:
+            if k in arguments and arguments[k] is not None:
+                query_params[k] = arguments[k]
+
+        # Add default parameters that are not shown in the schema
+        for k, v in self.default_params_not_shown.items():
+            if k not in query_params:
+                query_params[k] = v
+
+        if "description_type" in expected_param_names:
+            query_type = "description"
+            if query_params["description_type"].lower() == "full":
+                query_params["fields"] = [
+                    "NCTId",
+                    "BriefTitle",
+                    "OfficialTitle",
+                    "BriefSummary",
+                    "DetailedDescription",
+                    "Phase",
+                ]
+            else:
+                query_params["fields"] = [
+                    "NCTId",
+                    "BriefTitle",
+                    "BriefSummary",
+                    "Phase",
+                ]
+            del query_params["description_type"]
+        elif "status_and_date" in expected_param_names:
+            query_type = "status_and_date"
+            if "status_and_date" in query_params:
+                del query_params["status_and_date"]
+            query_params["fields"] = [
+                "NCTId",
+                "OverallStatus",
+                "LastKnownStatus",
+                "WhyStopped",
+                "StartDate",
+                "PrimaryCompletionDate",
+                "CompletionDate",
+            ]
+        elif "condition_and_intervention" in expected_param_names:
+            query_type = "condition_and_intervention"
+            if "condition_and_intervention" in query_params:
+                del query_params["condition_and_intervention"]
+            query_params["fields"] = [
+                "NCTId",
+                "Condition",
+                "ArmGroupLabel",
+                "ArmGroupType",
+                "ArmGroupDescription",
+                "ArmGroupInterventionName",
+                "InterventionType",
+                "InterventionName",
+                "InterventionOtherName",
+                "InterventionDescription",
+                # "InterventionArmGroupLabel",
+            ]
+        elif "eligibility_criteria" in expected_param_names:
+            query_type = "eligibility_criteria"
+            if "eligibility_criteria" in query_params:
+                del query_params["eligibility_criteria"]
+            query_params["fields"] = [
+                "NCTId",
+                "HealthyVolunteers",
+                "Sex",
+                "GenderBased",
+                "GenderDescription",
+                "MinimumAge",
+                "MaximumAge",
+                "StudyPopulation",
+                "EligibilityCriteria",
+                # "SamplingMethod",
+            ]
+        elif "location" in expected_param_names:
+            query_type = "location"
+            if "location" in query_params:
+                del query_params["location"]
+            query_params["fields"] = [
+                "NCTId",
+                "LocationFacility",
+                "LocationStatus",
+                "LocationCity",
+                "LocationState",
+                "LocationCountry",
+            ]
+        elif "outcome_measures" in expected_param_names:
+            query_type = "outcome_measures"
+            if query_params["outcome_measures"].lower() == "primary":
+                query_params["fields"] = [
+                    "NCTId",
+                    "PrimaryOutcome",
+                ]
+            elif query_params["outcome_measures"].lower() == "secondary":
+                query_params["fields"] = [
+                    "NCTId",
+                    "SecondaryOutcome",
+                ]
+            else:
+                query_params["fields"] = [
+                    "NCTId",
+                    "PrimaryOutcome",
+                    "SecondaryOutcome",
+                    # "OtherOutcome",
+                ]
+            del query_params["outcome_measures"]
+        elif "references" in expected_param_names:
+            query_type = "references"
+            if "references" in query_params:
+                del query_params["references"]
+            query_params["fields"] = [
+                "NCTId",
+                "Reference",
+                "SeeAlsoLink",
+            ]
+
+        # more difficult extractions here
+        elif "baseline_characteristics" in expected_param_names:
+            query_type = "baseline_characteristics"
+            del query_params["baseline_characteristics"]
+            query_params["fields"] = [
+                "NCTId",
+                "BaselineCharacteristicsModule",
+            ]
+            # TODO: Add this to the schema
+
+        elif "outcome_measure" in expected_param_names:
+            query_type = "outcome"
+            outcome_measure = query_params["outcome_measure"]
+            del query_params["outcome_measure"]
+            query_params["fields"] = [
+                "NCTId",
+                "OutcomeMeasure",
+            ]
+
+        elif "adverse_event_type" in expected_param_names:
+            query_type = "safety"
+            organs = query_params.get("organ_systems", [])
+            adverse_event_type = query_params.get("adverse_event_type", "serious")
+            if "organ_systems" in query_params:
+                del query_params["organ_systems"]
+            del query_params["adverse_event_type"]
+            query_params["fields"] = [
+                "NCTId",
+                "AdverseEventsModule",
+            ]
+
+        api_params = self._prepare_api_params(query_params)
+        formatted_endpoint_url = self.endpoint_url
+
+        responses = []
+        for nct_id in nct_ids_list:
+            formatted_endpoint_url = self._format_endpoint_url({"nctId": nct_id})
+            response = execute_RESTful_query(
+                endpoint_url=formatted_endpoint_url, variables=api_params
+            )
+            if response:
+                responses.append(response)
+
+        if query_type not in {"outcome", "safety"}:
+            responses = [
+                self._simplify_output(response, query_type) for response in responses
+            ]
+        elif query_type == "outcome":
+            responses = [
+                self._extract_outcomes_from_output(response, outcome_measure)
+                for response in responses
+            ]
+        elif query_type == "safety":
+            responses = [
+                self._extract_safety_from_output(response, organs, adverse_event_type)
+                for response in responses
+            ]
+
+        if sum([len(response) > 1 for response in responses]) == 0:
+            return "No relevant information found for the given NCT IDs."
+
+        return responses
+
+    def _simplify_output(self, study, query_type):
+        """Manually extract generally most useful information"""
+        new_study = {
+            "NCT ID": study["protocolSection"]["identificationModule"].get("nctId"),
+        }
+        if "identificationModule" in study["protocolSection"]:
+            if "briefTitle" in study["protocolSection"]["identificationModule"]:
+                new_study["brief_title"] = study["protocolSection"][
+                    "identificationModule"
+                ].get("briefTitle")
+            if "officialTitle" in study["protocolSection"]["identificationModule"]:
+                new_study["official_title"] = study["protocolSection"][
+                    "identificationModule"
+                ].get("officialTitle")
+        if "statusModule" in study["protocolSection"]:
+            if "overallStatus" in study["protocolSection"]["statusModule"]:
+                new_study["overall_status"] = study["protocolSection"][
+                    "statusModule"
+                ].get("overallStatus")
+            if "lastKnownStatus" in study["protocolSection"]["statusModule"]:
+                new_study["last_known_status"] = study["protocolSection"][
+                    "statusModule"
+                ].get("lastKnownStatus")
+            if "whyStopped" in study["protocolSection"]["statusModule"]:
+                new_study["why_stopped"] = study["protocolSection"]["statusModule"].get(
+                    "whyStopped"
+                )
+            if "startDateStruct" in study["protocolSection"]["statusModule"]:
+                new_study["start_date"] = study["protocolSection"]["statusModule"][
+                    "startDateStruct"
+                ].get("date")
+            if (
+                "primaryCompletionDateStruct"
+                in study["protocolSection"]["statusModule"]
+            ):
+                new_study["primary_completion_date"] = study["protocolSection"][
+                    "statusModule"
+                ]["primaryCompletionDateStruct"].get("date")
+            if "completionDateStruct" in study["protocolSection"]["statusModule"]:
+                new_study["completion_date"] = study["protocolSection"]["statusModule"][
+                    "completionDateStruct"
+                ].get("date")
+        if "descriptionModule" in study["protocolSection"]:
+            if "briefSummary" in study["protocolSection"]["descriptionModule"]:
+                new_study["brief_summary"] = study["protocolSection"][
+                    "descriptionModule"
+                ].get("briefSummary")
+            if "detailedDescription" in study["protocolSection"]["descriptionModule"]:
+                new_study["detailed_description"] = study["protocolSection"][
+                    "descriptionModule"
+                ].get("detailedDescription")
+        if "conditionsModule" in study["protocolSection"]:
+            if "conditions" in study["protocolSection"]["conditionsModule"]:
+                new_study["condition"] = study["protocolSection"][
+                    "conditionsModule"
+                ].get("conditions")
+        if "designModule" in study["protocolSection"]:
+            if "phases" in study["protocolSection"]["designModule"]:
+                new_study["phase"] = study["protocolSection"]["designModule"].get(
+                    "phases"
+                )
+            if "patientRegistry" in study["protocolSection"]["designModule"]:
+                new_study["patient_registry"] = study["protocolSection"][
+                    "designModule"
+                ].get("patientRegistry")
+            if "enrollmentInfo" in study["protocolSection"]["designModule"]:
+                new_study["enrollment_info"] = study["protocolSection"][
+                    "designModule"
+                ].get("enrollmentInfo")
+        if "armsInterventionsModule" in study["protocolSection"]:
+            if "armGroups" in study["protocolSection"]["armsInterventionsModule"]:
+                new_study["arm_groups"] = study["protocolSection"][
+                    "armsInterventionsModule"
+                ].get("armGroups")
+            if "interventions" in study["protocolSection"]["armsInterventionsModule"]:
+                new_study["interventions"] = study["protocolSection"][
+                    "armsInterventionsModule"
+                ].get("interventions")
+        if "outcomesModule" in study["protocolSection"]:
+            if "primaryOutcomes" in study["protocolSection"]["outcomesModule"]:
+                new_study["primary_outcomes"] = study["protocolSection"][
+                    "outcomesModule"
+                ].get("primaryOutcomes")
+            if "secondaryOutcomes" in study["protocolSection"]["outcomesModule"]:
+                new_study["secondary_outcomes"] = study["protocolSection"][
+                    "outcomesModule"
+                ].get("secondaryOutcomes")
+            # if "otherOutcomes" in study["protocolSection"]["outcomesModule"]:
+            #     new_study["other_outcomes"] = study["protocolSection"]["outcomesModule"].get("otherOutcomes")
+        if "eligibilityModule" in study["protocolSection"]:
+            if "eligibilityCriteria" in study["protocolSection"]["eligibilityModule"]:
+                new_study["eligibility_criteria"] = study["protocolSection"][
+                    "eligibilityModule"
+                ].get("eligibilityCriteria")
+            if "healthyVolunteers" in study["protocolSection"]["eligibilityModule"]:
+                new_study["healthy_volunteers"] = study["protocolSection"][
+                    "eligibilityModule"
+                ].get("healthyVolunteers")
+            if "sex" in study["protocolSection"]["eligibilityModule"]:
+                new_study["sex"] = study["protocolSection"]["eligibilityModule"].get(
+                    "sex"
+                )
+            if "genderBased" in study["protocolSection"]["eligibilityModule"]:
+                new_study["gender_based"] = study["protocolSection"][
+                    "eligibilityModule"
+                ].get("genderBased")
+            if "genderDescription" in study["protocolSection"]["eligibilityModule"]:
+                new_study["gender_description"] = study["protocolSection"][
+                    "eligibilityModule"
+                ].get("genderDescription")
+            if "minimumAge" in study["protocolSection"]["eligibilityModule"]:
+                new_study["minimum_age"] = study["protocolSection"][
+                    "eligibilityModule"
+                ].get("minimumAge")
+            if "maximumAge" in study["protocolSection"]["eligibilityModule"]:
+                new_study["maximum_age"] = study["protocolSection"][
+                    "eligibilityModule"
+                ].get("maximumAge")
+            if "studyPopulation" in study["protocolSection"]["eligibilityModule"]:
+                new_study["study_population"] = study["protocolSection"][
+                    "eligibilityModule"
+                ].get("studyPopulation")
+            # if "samplingMethod" in study["protocolSection"]["eligibilityModule"]:
+            #     new_study["sampling_method"] = study["protocolSection"]["eligibilityModule"].get("samplingMethod")
+        if "contactsLocationsModule" in study["protocolSection"]:
+            if "locations" in study["protocolSection"]["contactsLocationsModule"]:
+                new_study["locations"] = study["protocolSection"][
+                    "contactsLocationsModule"
+                ].get("locations")
+        if "referencesModule" in study["protocolSection"]:
+            if "references" in study["protocolSection"]["referencesModule"]:
+                new_study["references"] = study["protocolSection"][
+                    "referencesModule"
+                ].get("references")
+            if "seeAlsoLinks" in study["protocolSection"]["referencesModule"]:
+                new_study["see_also_links"] = study["protocolSection"][
+                    "referencesModule"
+                ].get("seeAlsoLinks")
+
+        new_study = self._remove_empty_values(new_study)
+
+        return new_study
+
+    def _extract_outcomes_from_output(self, study, outcome_measure):
+        new_study = {}
+        outcome_measure = outcome_measure.lower()
+        new_study["NCT ID"] = study["protocolSection"]["identificationModule"].get(
+            "nctId"
+        )
+
+        if (
+            "resultsSection" in study
+            and "outcomeMeasuresModule" in study["resultsSection"]
+            and "outcomeMeasures" in study["resultsSection"]["outcomeMeasuresModule"]
+        ):
+            raw_outcomes = study["resultsSection"]["outcomeMeasuresModule"][
+                "outcomeMeasures"
+            ]
+            outcomes = []
+            for outcome in raw_outcomes:
+                new_outcome = {}
+
+                if (outcome_measure == "primary") and outcome.get("type") != "PRIMARY":
+                    continue
+                if (outcome_measure == "secondary") and outcome.get(
+                    "type"
+                ) != "SECONDARY":
+                    continue
+                if (outcome_measure == "all") and outcome.get("type") not in [
+                    "PRIMARY",
+                    "SECONDARY",
+                ]:
+                    continue
+                if outcome_measure not in ["primary", "secondary", "all"]:
+                    outcome_measure_variants = [outcome_measure]
+                    # TODO: Add more rules here
+                    outcome_measure_variants.append(outcome_measure.replace("-", " "))
+                    outcome_measure_variants.append(outcome_measure.replace(" ", "-"))
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("progression", "progress")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("progress ", "progression ")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("progress-", "progression-")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("patient", "participant")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("participant", "patient")
+                    )
+                    outcome_measure_variants.append(outcome_measure.replace("_", " "))
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("percentage", "percent")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("percent ", "percentage ")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("percent-", "percentage-")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("proportion", "percentage")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("percentage", "proportion")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("proportion", "percent")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("percent", "proportion")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("time to event", "time-to-event")
+                    )
+                    outcome_measure_variants.append(
+                        outcome_measure.replace("time-to-event", "time to event")
+                    )
+                    outcome_measure_variants = list(set(outcome_measure_variants))
+                    found_match = False
+                    for o in outcome_measure_variants:
+                        if (
+                            o in outcome.get("title", "").lower()
+                            or o in outcome.get("description", "").lower()
+                        ):
+                            found_match = True
+                            break
+                    if not found_match:
+                        continue
+
+                new_outcome["title"] = outcome.get("title")
+                new_outcome["description"] = outcome.get("description")
+                new_outcome["population"] = outcome.get("populationDescription")
+                new_outcome["time_frame"] = outcome.get("timeFrame")
+                new_outcome["unit_analyzed"] = outcome.get("typeUnitsAnalyzed")
+
+                measurement_type = outcome.get("paramType")
+                if measurement_type:
+                    measurement_type = measurement_type.lower()
+                # GEOMETRIC_MEAN - Geometric Mean
+                # GEOMETRIC_LEAST_SQUARES_MEAN - Geometric Least Squares Mean
+                # LEAST_SQUARES_MEAN - Least Squares Mean
+                # LOG_MEAN - Log Mean
+                # MEAN - Mean
+                # MEDIAN - Median
+                # NUMBER - Number
+                # COUNT_OF_PARTICIPANTS - Count of Participants
+                # COUNT_OF_UNITS - Count of Units
+
+                unit = outcome.get("unitOfMeasure")
+
+                new_outcome["groups"] = outcome.get("groups")
+
+                denoms = outcome.get("denoms")
+                if denoms is not None:
+                    if len(denoms) > 1:
+                        # TODO: Investigate such trials
+                        return f"Warning: Multiple denoms found for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                    denoms = denoms[0]["counts"]
+                    new_outcome["denominators"] = denoms
+
+                classes = outcome.get("classes")
+                if classes is not None:
+                    if len(classes) > 1:
+                        # TODO: Investigate such trials
+                        return f"Warning: Multiple classes found for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                    if "title" in classes[0] or "denoms" in classes[0]:
+                        # TODO: Investigate such trials
+                        return f"Warning: Unexpected structure in classes for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                        classes = classes[0]
+                    elif "categories" in classes[0]:
+                        classes = classes[0]["categories"]
+                        if len(classes) > 1:
+                            # TODO: Investigate such trials
+                            return f"Warning: Multiple classes-categories found for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                        if "title" in classes[0]:
+                            # TODO: Investigate such trials
+                            return f"Warning: Unexpected structure in classes-categories for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                            classes = classes[0]
+                        elif "measurements" in classes[0]:
+                            classes = classes[0]["measurements"]
+                        else:
+                            # TODO: Investigate such trials
+                            return f"Warning: Unexpected structure in classes-categories for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                    else:
+                        # TODO: Investigate such trials
+                        return f"Warning: Unexpected structure in classes for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+
+                    if measurement_type and unit:
+                        new_outcome[measurement_type + " (" + unit + ")"] = classes
+                    else:
+                        # TODO: Investigate such trials
+                        return f"Warning: Missing paramType or unitOfMeasure for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+
+                analyses = outcome.get("analyses")
+                if analyses is not None:
+                    if len(analyses) > 1:
+                        # TODO: Investigate such trials
+                        return f"Warning: Multiple analyses found for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                    analyses = analyses[0]
+                    pvalue = analyses.get("pValue")
+                    pvalue_comment = analyses.get("pValueComment")
+                    statistic_test = analyses.get("statisticalMethod")
+                    statistic_comment = analyses.get("statisticalComment")
+
+                    statistic_name = analyses.get("paramType")
+                    statistic = analyses.get("paramValue")
+                    if statistic_name and statistic_test and statistic and pvalue:
+                        new_outcome["p-value (" + statistic_test + ")"] = pvalue
+                        new_outcome[statistic_name] = statistic
+                    else:
+                        # TODO: Investigate such trials
+                        return f"Warning: Missing paramType, paramValue, statisticalMethod or pvalue for outcome {new_outcome['title']} in study {new_study['NCT ID']}."
+                    if statistic_comment:
+                        new_outcome["statistic_comment"] = statistic_comment
+                    if pvalue_comment:
+                        new_outcome["pvalue_comment"] = pvalue_comment
+
+                    statistic_test_type = analyses.get("nonInferiorityType")
+                    statistic_test_type_comment = analyses.get(
+                        "nonInferiorityTypeComment"
+                    )
+                    if statistic_test_type and statistic_test_type_comment:
+                        new_outcome["statistic_test_type"] = statistic_test_type
+                        new_outcome["statistic_test_type_comment"] = (
+                            statistic_test_type_comment
+                        )
+
+                outcomes.append(new_outcome)
+
+            new_study["outcomes"] = outcomes
+            new_study = self._remove_empty_values(new_study)
+
+        return new_study
+
+    def _extract_safety_from_output(self, study, organs, adverse_event_type):
+        new_study = {}
+        adverse_event_type = adverse_event_type.lower()
+        organs = [org.lower() for org in organs]
+        new_study["NCT ID"] = study["protocolSection"]["identificationModule"].get(
+            "nctId"
+        )
+
+        if (
+            "resultsSection" in study
+            and "adverseEventsModule" in study["resultsSection"]
+        ):
+            ae_data = study["resultsSection"]["adverseEventsModule"]
+            new_study["freq_threshold"] = (
+                ae_data["frequencyThreshold"] + "%"
+                if "frequencyThreshold" in ae_data
+                else None
+            )
+            groups = ae_data["eventGroups"]
+            for group in groups:
+                if "deathsNumAffected" in group:
+                    del group["deathsNumAffected"]
+                if "deathsNumAtRisk" in group:
+                    del group["deathsNumAtRisk"]
+            #     if "seriousNumAffected" in group:
+            #         del group["seriousNumAffected"]
+            #     if "seriousNumAtRisk" in group:
+            #         del group["seriousNumAtRisk"]
+            #     if "otherNumAffected" in group:
+            #         del group["otherNumAffected"]
+            #     if "otherNumAtRisk" in group:
+            #         del group["otherNumAtRisk"]
+
+            new_study["groups"] = groups
+
+            if "seriousEvents" in ae_data and adverse_event_type != "other":
+                raw_aes = ae_data["seriousEvents"]
+                serious_aes = []
+                for ae in raw_aes:
+                    if adverse_event_type not in {"serious", "all"}:
+                        ae_name = ae.get("term", "").lower()
+                        if adverse_event_type not in ae_name:
+                            continue
+                    if len(organs) > 0:
+                        organ_system = ae.get("organSystem", "").lower()
+                        if organ_system not in organs:
+                            continue
+
+                    if "sourceVocabulary" in ae:
+                        del ae["sourceVocabulary"]
+                    if "assessmentType" in ae:
+                        del ae["assessmentType"]
+
+                    if "stats" in ae and len(ae["stats"]) > 0:
+                        for group_stats in ae["stats"]:
+                            if (
+                                group_stats.get("numAffected") is not None
+                                and group_stats.get("numAtRisk") is not None
+                                and group_stats.get("numAtRisk", 0) > 0
+                            ):
+                                group_stats["percentage"] = (
+                                    str(
+                                        round(
+                                            group_stats.get("numAffected", 0)
+                                            / group_stats.get("numAtRisk", 1)
+                                            * 100,
+                                            2,
+                                        )
+                                    )
+                                    + "%"
+                                )
+                            elif (
+                                group_stats.get("numEvents") is not None
+                                and group_stats.get("numAtRisk") is not None
+                                and group_stats.get("numAtRisk", 0) > 0
+                            ):
+                                group_stats["percentage"] = (
+                                    str(
+                                        round(
+                                            group_stats.get("numEvents", 0)
+                                            / group_stats.get("numAtRisk", 1)
+                                            * 100,
+                                            2,
+                                        )
+                                    )
+                                    + "%"
+                                )
+                            else:
+                                group_stats["percentage"] = None
+
+                            if "numEvents" in group_stats:
+                                del group_stats["numEvents"]
+
+                    serious_aes.append(ae)
+
+                new_study["serious_adverse_events"] = serious_aes
+
+            if "otherEvents" in ae_data and adverse_event_type != "serious":
+                raw_aes = ae_data["otherEvents"]
+                other_aes = []
+                for ae in raw_aes:
+                    if adverse_event_type not in {"other", "all"}:
+                        ae_name = ae.get("term", "").lower()
+                        if adverse_event_type not in ae_name:
+                            continue
+                    if len(organs) > 0:
+                        organ_system = ae.get("organSystem", "").lower()
+                        if organ_system not in organs:
+                            continue
+
+                    if "sourceVocabulary" in ae:
+                        del ae["sourceVocabulary"]
+                    if "assessmentType" in ae:
+                        del ae["assessmentType"]
+
+                    if "stats" in ae and len(ae["stats"]) > 0:
+                        for group_stats in ae["stats"]:
+                            if (
+                                group_stats.get("numAffected") is not None
+                                and group_stats.get("numAtRisk") is not None
+                                and group_stats.get("numAtRisk", 0) > 0
+                            ):
+                                group_stats["percentage"] = (
+                                    str(
+                                        round(
+                                            group_stats.get("numAffected", 0)
+                                            / group_stats.get("numAtRisk", 1)
+                                            * 100,
+                                            2,
+                                        )
+                                    )
+                                    + "%"
+                                )
+                            elif (
+                                group_stats.get("numEvents") is not None
+                                and group_stats.get("numAtRisk") is not None
+                                and group_stats.get("numAtRisk", 0) > 0
+                            ):
+                                group_stats["percentage"] = (
+                                    str(
+                                        round(
+                                            group_stats.get("numeEvents", 0)
+                                            / group_stats.get("numAtRisk", 1)
+                                            * 100,
+                                            2,
+                                        )
+                                    )
+                                    + "%"
+                                )
+                            else:
+                                group_stats["percentage"] = None
+
+                            if "numEvents" in group_stats:
+                                del group_stats["numEvents"]
+
+                    other_aes.append(ae)
+
+                new_study["other_adverse_events"] = other_aes
+
+            new_study = self._remove_empty_values(new_study)
+
+        return new_study
+
+    def _remove_empty_values(self, obj):
+        if isinstance(obj, dict):
+            return {
+                k: self._remove_empty_values(v)
+                for k, v in obj.items()
+                if v not in [[], None]
+            }
+        elif isinstance(obj, list):
+            return [self._remove_empty_values(v) for v in obj if v not in [[], None]]
+        else:
+            return obj