diff --git a/.gitignore b/.gitignore
index 4c454286..bb2539fd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,4 @@ nmdc_automation/workflow_automation/_state/*.json
 
 # Ignore `coverage.xml` file in this directory.
 /coverage.xml
+prof/
diff --git a/nmdc_automation/__init__.py b/nmdc_automation/__init__.py
index 0dd591c9..356b0118 100644
--- a/nmdc_automation/__init__.py
+++ b/nmdc_automation/__init__.py
@@ -2,3 +2,4 @@
 from .config import siteconfig
 from .import_automation import activity_mapper
 from .workflow_automation import watch_nmdc, wfutils, workflows, workflow_process
+from .models import workflow, nmdc
diff --git a/nmdc_automation/api/nmdcapi.py b/nmdc_automation/api/nmdcapi.py
index 15efb92c..78d3adc2 100755
--- a/nmdc_automation/api/nmdcapi.py
+++ b/nmdc_automation/api/nmdcapi.py
@@ -193,6 +193,8 @@ def post_objects(self, obj_data):
         url = self._base_url + "workflows/workflow_executions"
 
         resp = requests.post(url, headers=self.header, data=json.dumps(obj_data))
+        if not resp.ok:
+            resp.raise_for_status()
         return resp.json()
 
     @refresh_token
@@ -320,6 +322,8 @@ def update_op(self, opid, done=None, results=None, meta=None):
     def run_query(self, query):
         url = "%squeries:run" % self._base_url
         resp = requests.post(url, headers=self.header, data=json.dumps(query))
+        if not resp.ok:
+            resp.raise_for_status()
         return resp.json()
 
 
diff --git a/nmdc_automation/import_automation/activity_mapper.py b/nmdc_automation/import_automation/activity_mapper.py
index 1226855e..303c1725 100644
--- a/nmdc_automation/import_automation/activity_mapper.py
+++ b/nmdc_automation/import_automation/activity_mapper.py
@@ -13,6 +13,7 @@
 
 from linkml_runtime.dumpers import json_dumper
 from nmdc_automation.api import NmdcRuntimeApi
+from nmdc_automation.models.nmdc import DataObject, workflow_process_factory
 from .utils import object_action, file_link, get_md5, filter_import_by_type
 
 logger = logging.getLogger(__name__)
@@ -26,7 +27,7 @@ def __init__(
         nucelotide_sequencing_id: str,
         yaml_file: Union[str, Path],
         project_directory: Union[str, Path],
-        site_config_file: Union[str, Path],
+        runtime: NmdcRuntimeApi,
     ):
         """
         Initialize the GoldMapper object.
@@ -39,9 +40,7 @@ def __init__(
             project_directory: Project directory path.
         """
 
-        with open(yaml_file, "r") as file:
-            self.import_data = yaml.safe_load(file)
-
+        self.import_data = self.load_yaml_file(yaml_file)
         self.nmdc_db = nmdc.Database()
         self.iteration = iteration
         self.file_list = file_list
@@ -52,140 +51,170 @@ def __init__(
         self.project_dir = project_directory
         self.url = self.import_data["Workflow Metadata"]["Source URL"]
         self.data_object_type = "nmdc:DataObject"
-        self.objects = {}
+        self.data_object_map = {}
         self.workflow_execution_ids = {}
-        self.workflows_by_type = {}
+        self.workflows_by_type = self.build_workflows_by_type()
+        self.runtime = runtime
 
-        self.runtime = NmdcRuntimeApi(site_config_file)
 
-        for wf in self.import_data["Workflows"]:
-            self.workflows_by_type[wf["Type"]] = wf
+    def load_yaml_file(self, yaml_file: Union[str, Path]) -> Dict:
+        """Utility function to load YAML file."""
+        with open(yaml_file, "r") as file:
+            return yaml.safe_load(file)
+
+    def build_workflows_by_type(self) -> Dict:
+        """Builds a dictionary of workflows by their type."""
+        return {wf["Type"]: wf for wf in self.import_data["Workflows"]}
 
-    def unique_object_mapper(self) -> None:
+    def map_sequencing_data(self) -> Tuple[nmdc.Database, Dict]:
         """
-        Map unique data objects from the file list based on unique matching import suffix.
-        The method relates each object to an workflow execution ID and updates the file with object action.
-        It updates the nmdc database with the DataObject and stores the information in the objects dictionary.
+        Map sequencing data to an NMDC data object and create an update to be applied to the has_output
+        list of the sequencing data generation.
         """
-
-        for data_object_dict in self.import_data["Data Objects"]["Unique"]:
-            if not filter_import_by_type(
-                self.import_data["Workflows"], data_object_dict["output_of"]
-            ):
-                continue
-            for file in self.file_list:
-                file = str(file)
-                if data_object_dict is None:
-                    continue
-                elif "import_suffix" not in data_object_dict:
-                    logging.warning("Missing suffix")
-                    continue
-
-                elif re.search(data_object_dict["import_suffix"], file):
-                    workflow_execution_id = self.get_workflow_execution_id(data_object_dict["output_of"])
-
+        # Define the sequencing types to look for -
+        sequencing_types = ["Metagenome Raw Reads",]
+        db = nmdc.Database()
+
+        # get the Metagenome Raw Reads import data
+        sequencing_import_data = [
+            d for d in self.import_data["Data Objects"]["Unique"] if d["data_object_type"] in sequencing_types
+        ]
+        has_output = []
+        for data_object_dict in sequencing_import_data:
+            # get the file(s) that match the import suffix
+            for import_file in self.file_list:
+                import_file = str(import_file)
+                if re.search(data_object_dict["import_suffix"], import_file):
+                    logging.debug(f"Processing {data_object_dict['data_object_type']}")
                     file_destination_name = object_action(
-                        file,
+                        import_file,
                         data_object_dict["action"],
-                        workflow_execution_id,
+                        self.nucelotide_sequencing_id,
                         data_object_dict["nmdc_suffix"],
                     )
-
-                    workflow_execution_dir = os.path.join(self.root_dir, workflow_execution_id)
-
-                    updated_file = file_link(
-                        self.project_dir, file, workflow_execution_dir, file_destination_name
-                    )
-
-                    filemeta = os.stat(updated_file)
-
-                    md5 = get_md5(updated_file)
-
-                    dobj = self.runtime.minter(self.data_object_type)
-
-                    self.nmdc_db.data_object_set.append(
-                        nmdc.DataObject(
-                            file_size_bytes=filemeta.st_size,
-                            name=file_destination_name,
-                            url=f"{self.url}/{self.nucelotide_sequencing_id}/{workflow_execution_id}/{file_destination_name}",
-                            data_object_type=data_object_dict["data_object_type"],
-                            type=self.data_object_type,
-                            id=dobj,
-                            md5_checksum=md5,
-                            description=data_object_dict["description"].replace(
-                                "{id}", self.nucelotide_sequencing_id
-                            ),
+                    # sequencing_dir = os.path.join(self.root_dir, self.nucelotide_sequencing_id)
+                    try:
+                        os.makedirs(self.root_dir)
+                    except FileExistsError:
+                        logger.debug(f"{self.root_dir} already exists")
+
+                    export_file = os.path.join(self.root_dir, file_destination_name)
+
+                    try:
+                        os.link(import_file, export_file)
+                    except FileExistsError:
+                        logger.debug(f"{export_file} already exists")
+
+                    filemeta = os.stat(export_file)
+                    md5 = get_md5(export_file)
+                    data_object_id = self.runtime.minter(self.data_object_type)
+                    # Imported nucleotide sequencing data object does not have a URL
+                    do_record = {
+                        "id": data_object_id,
+                        "type": self.data_object_type,
+                        "name": file_destination_name,
+                        "file_size_bytes": filemeta.st_size,
+                        "md5_checksum": md5,
+                        "data_object_type": data_object_dict["data_object_type"],
+                        "description": data_object_dict["description"].replace(
+                            "{id}", self.nucelotide_sequencing_id
                         )
-                    )
-                    self.objects[data_object_dict["data_object_type"]] = (
-                        data_object_dict["input_to"],
-                        [data_object_dict["output_of"]],
-                        dobj,
-                    )
+                    }
+                    db.data_object_set.append(DataObject(**do_record))
+                    has_output.append(data_object_id)
+        update = {
+            "collection": "data_generation_set",
+            "filter": {"id": self.nucelotide_sequencing_id},
+            "update": {"$addToSet": {"has_output": has_output}}
+        }
+        # update self.data_object_map
+        if len(has_output) > 1:
+            raise ValueError("More than one sequencing data object found")
+        self.data_object_map["Metagenome Raw Reads"] = (
+            ["nmdc:ReadQcAnalysis"], ["nmdc:NucleotideSequencing"], has_output[0]
+        )
+        return db, update
 
-    def multiple_objects_mapper(self) -> None:
+
+    def map_data(self,db: nmdc.Database, unique: bool = True) -> Tuple[nmdc.Database, Dict]:
         """
-        Maps multiple data objects from the file list based on matching import suffix into one nmdc data object.
-        The method relates each object to an workflow execution ID and updates the file with object action.
-        It updates the nmdc database with the DataObject and stores the information in the objects dictionary.
+        Map data objects to the NMDC database.
         """
 
-        multiple_objects_list = []
-
-        for data_object_dict in self.import_data["Data Objects"]["Multiples"]:
-            for file in self.file_list:
-                file = str(file)
-                if re.search(data_object_dict["import_suffix"], file):
-                    multiple_objects_list.append(file)
-
-            workflow_execution_id = self.get_workflow_execution_id(data_object_dict["output_of"])
-
-            workflow_execution_dir = os.path.join(self.root_dir, workflow_execution_id)
-
+        def process_files(files: Union[str, List[str]], data_object_dict: Dict, workflow_execution_id: str,
+                          multiple: bool = False) -> DataObject:
+            """
+            Process import file(s) and return a DataObject instance. Map data object ids to input_to and
+            output_of workflow execution types.
+            """
             file_destination_name = object_action(
-                multiple_objects_list,
+                files,
                 data_object_dict["action"],
                 workflow_execution_id,
                 data_object_dict["nmdc_suffix"],
-                workflow_execution_dir=workflow_execution_dir,
-                multiple=True,
+                workflow_execution_dir=os.path.join(self.root_dir, workflow_execution_id),
+                multiple=multiple,
             )
-
             updated_file = file_link(
                 self.project_dir,
-                multiple_objects_list,
-                workflow_execution_dir,
+                files,
+                os.path.join(self.root_dir, workflow_execution_id),
                 file_destination_name,
             )
-
             filemeta = os.stat(updated_file)
-
             md5 = get_md5(updated_file)
-
-            dobj = self.runtime.minter(self.data_object_type)
-
-            self.nmdc_db.data_object_set.append(
-                nmdc.DataObject(
-                    file_size_bytes=filemeta.st_size,
-                    name=data_object_dict["name"],
-                    url=f"{self.url}/{self.nucelotide_sequencing_id}/{workflow_execution_id}/{file_destination_name}",
-                    data_object_type=data_object_dict["data_object_type"],
-                    type=self.data_object_type,
-                    id=dobj,
-                    md5_checksum=md5,
-                    description=data_object_dict["description"].replace(
-                        "{id}", self.nucelotide_sequencing_id
-                    ),
+            data_object_id = self.runtime.minter(self.data_object_type)
+            do_record = {
+                "id": data_object_id,
+                "type": self.data_object_type,
+                "name": file_destination_name,
+                "url": f"{self.url}/{self.nucelotide_sequencing_id}/{workflow_execution_id}/{file_destination_name}",
+                "file_size_bytes": filemeta.st_size,
+                "md5_checksum": md5,
+                "data_object_type": data_object_dict["data_object_type"],
+                "description": data_object_dict["description"].replace(
+                    "{id}", self.nucelotide_sequencing_id
                 )
-            )
-
-            self.objects[data_object_dict["data_object_type"]] = (
+            }
+            # update self.objects mapping
+            self.data_object_map[data_object_dict["data_object_type"]] = (
                 data_object_dict["input_to"],
                 [data_object_dict["output_of"]],
-                dobj,
+                data_object_id,
             )
+            return DataObject(**do_record)
+
+        # Select the correct data source (unique or multiple)
+        data_objects_key = "Unique" if unique else "Multiples"
+        data_object_specs = self.import_data["Data Objects"][data_objects_key]
+        for data_object_spec in data_object_specs:
+            if not filter_import_by_type(self.import_data["Workflows"], data_object_spec["output_of"]):
+                continue
+            if not "import_suffix" in data_object_spec:
+                logging.warning("Missing suffix")
+                continue
+
+            # Process unique data objects
+            if unique:
+                for file in map(str, self.file_list):
+                    if re.search(data_object_spec["import_suffix"], file):
+                        workflow_execution_id = self.get_workflow_execution_id(data_object_spec["output_of"])
+                        db.data_object_set.append(process_files(file, data_object_spec, workflow_execution_id))
+
+            # Process multiple data data files into a single data object
+            else:
+                multiple_files = []
+                for file in map(str, self.file_list):
+                    if re.search(data_object_spec["import_suffix"], file):
+                        multiple_files.append(file)
+                if multiple_files:
+                    workflow_execution_id = self.get_workflow_execution_id(data_object_spec["output_of"])
+                    db.data_object_set.append(process_files(multiple_files, data_object_spec, workflow_execution_id, multiple=True))
 
-    def workflow_execution_mapper(self) -> None:
+        return db, self.data_object_map
+
+
+    def map_workflow_executions(self, db) -> nmdc.Database:
         """
         Maps workflow executions from the import data to the NMDC database.
         The function creates a database workflow execution set for each workflow type in the import data,
@@ -200,39 +229,45 @@ def workflow_execution_mapper(self) -> None:
             if not workflow.get("Import"):
                 continue
             logging.info(f"Processing {workflow['Name']}")
+
+            # Get the input / output lists for the workflow execution type
             has_inputs_list, has_output_list = self.attach_objects_to_workflow_execution(
                 workflow["Type"]
             )
-            # quick fix because nmdc-schema does not support [], even though raw product has none
-            if len(has_output_list) == 0:
-                logging.warning("No outputs.  That seems odd.")
-                has_output_list = ["None"]
-            # input may be none for metagenome sequencing
-            if len(has_inputs_list) == 0:
-                has_inputs_list = ["None"]
-            # Lookup the nmdc database class
-            database_workflow_execution_set = getattr(self.nmdc_db, workflow["Collection"])
-            # Lookup the nmdc schema range class
-            database_workflow_execution_range = getattr(nmdc, workflow["WorkflowExecutionRange"])
-            # Mint an ID
-            workflow_execution_id = self.get_workflow_execution_id(workflow["Type"])
-            database_workflow_execution_set.append(
-                database_workflow_execution_range(
-                    id=workflow_execution_id,
-                    name=workflow["Workflow_Execution"]["name"].replace("{id}", workflow_execution_id),
-                    git_url=workflow["Git_repo"],
-                    version=workflow["Version"],
-                    execution_resource=self.import_data["Workflow Metadata"][
-                        "Execution Resource"
-                    ],
-                    started_at_time=datetime.datetime.now(pytz.utc).isoformat(),
-                    has_input=has_inputs_list,
-                    has_output=has_output_list,
-                    type=workflow["Type"],
-                    ended_at_time=datetime.datetime.now(pytz.utc).isoformat(),
-                    was_informed_by=self.nucelotide_sequencing_id,
+            # We can't make a valid workflow execution without inputs and outputs
+            if not has_inputs_list or not has_output_list:
+                logging.error(
+                    f"Skipping {workflow['Name']} due to missing inputs or outputs"
                 )
-            )
+                continue
+            # Mint an ID if needed
+            wf_id = self.workflow_execution_ids.get(workflow["Type"], None)
+            if wf_id is None:
+                # mint an ID
+                wf_id = self.runtime.minter(workflow["Type"]) + "." + self.iteration
+                # store the ID
+                self.workflow_execution_ids[workflow["Type"]] = wf_id
+
+
+            # Create the workflow execution object
+            record = {
+                "id": wf_id,
+                "name": workflow["Workflow_Execution"]["name"].replace("{id}", wf_id),
+                "type": workflow["Type"],
+                "has_input": has_inputs_list,
+                "has_output": has_output_list,
+                "git_url": workflow["Git_repo"],
+                "version": workflow["Version"],
+                "execution_resource": self.import_data["Workflow Metadata"]["Execution Resource"],
+                "started_at_time": datetime.datetime.now(pytz.utc).isoformat(),
+                "ended_at_time": datetime.datetime.now(pytz.utc).isoformat(),
+                "was_informed_by": self.nucelotide_sequencing_id
+            }
+            wfe = workflow_process_factory(record)
+            db.workflow_execution_set.append(wfe)
+
+        return db
+
 
     def get_workflow_execution_id(self, output_of: str) -> str:
         """Lookup and returns minted workflow execution id
@@ -269,40 +304,14 @@ def attach_objects_to_workflow_execution(
             workflow execution type.
         """
 
-        data_object_outputs_of_list = []
-
-        data_object_inputs_to_list = []
+        has_input = []
+        has_output = []
 
-        for _, data_object_items in self.objects.items():
-            if workflow_execution_type in data_object_items[1]:
-                data_object_outputs_of_list.append(data_object_items[2])
-            elif workflow_execution_type in data_object_items[0]:
-                data_object_inputs_to_list.append(data_object_items[2])
+        for _, data_object_items in self.data_object_map.items():
+            input_types, ouput_types, data_object_id = data_object_items
+            if workflow_execution_type in input_types:
+                has_input.append(data_object_id)
+            if workflow_execution_type in ouput_types:
+                has_output.append(data_object_id)
 
-        return data_object_inputs_to_list, data_object_outputs_of_list
-
-    def post_nmdc_database_object(self) -> Dict:
-        """
-        Post the nmdc database object.
-
-        This function dumps the NMDC database object into JSON format, then posts
-        it using the runtime API.
-
-        Returns:
-            Dict: The response from the runtime API after posting the object.
-        """
-
-        nmdc_database_object = json.loads(
-            json_dumper.dumps(self.nmdc_db, inject_type=False)
-        )
-        res = self.runtime.post_objects(nmdc_database_object)
-        return res
-
-    def get_database_object_dump(self) -> nmdc.Database:
-        """
-        Get the NMDC database object.
-
-        Returns:
-            nmdc.Database: NMDC database object.
-        """
-        return self.nmdc_db
+        return has_input, has_output
diff --git a/nmdc_automation/import_automation/utils.py b/nmdc_automation/import_automation/utils.py
index 73007e3c..e818cd43 100644
--- a/nmdc_automation/import_automation/utils.py
+++ b/nmdc_automation/import_automation/utils.py
@@ -145,7 +145,7 @@ def file_link(
         linked_path = os.path.join(destination_dir, updated_file)
 
         try:
-            os.link(original_path, linked_path)
+            os.link(import_file, linked_path)
         except FileExistsError:
             logger.info(f"{linked_path} already exists")
 
diff --git a/nmdc_automation/models/__init__.py b/nmdc_automation/models/__init__.py
new file mode 100644
index 00000000..ea870490
--- /dev/null
+++ b/nmdc_automation/models/__init__.py
@@ -0,0 +1 @@
+""" Data classes for NMDC automation. """
\ No newline at end of file
diff --git a/nmdc_automation/models/nmdc.py b/nmdc_automation/models/nmdc.py
new file mode 100644
index 00000000..0b964474
--- /dev/null
+++ b/nmdc_automation/models/nmdc.py
@@ -0,0 +1,119 @@
+""" Factory methods for NMDC models. """
+import importlib.resources
+from typing import Any, Dict, Union
+import linkml_runtime
+import linkml.validator
+import importlib.resources
+from functools import lru_cache
+from linkml_runtime.dumpers import yaml_dumper
+import yaml
+
+
+from nmdc_schema.nmdc import DataGeneration, FileTypeEnum, MagsAnalysis, MetagenomeAnnotation, MetagenomeAssembly, \
+    MetatranscriptomeAnnotation, MetatranscriptomeAssembly, MetatranscriptomeExpressionAnalysis, NucleotideSequencing, \
+    ReadBasedTaxonomyAnalysis, ReadQcAnalysis, WorkflowExecution
+import nmdc_schema.nmdc as nmdc
+
+
+@lru_cache(maxsize=None)
+def get_nmdc_materialized():
+    with importlib.resources.open_text("nmdc_schema", "nmdc_materialized_patterns.yaml") as f:
+        return yaml.safe_load(f)
+
+def workflow_process_factory(record: Dict[str, Any], validate: bool = False) -> Union[DataGeneration,
+WorkflowExecution]:
+    """
+    Factory function to create a PlannedProcess subclass object from a record.
+    Subclasses are determined by the "type" field in the record, and can be
+    either a WorkflowExecution or DataGeneration object.
+    """
+    nmdc_materialized = get_nmdc_materialized()
+    process_types = {
+        "nmdc:MagsAnalysis": MagsAnalysis,
+        "nmdc:MetagenomeAnnotation": MetagenomeAnnotation,
+        "nmdc:MetagenomeAssembly": MetagenomeAssembly,
+        "nmdc:MetatranscriptomeAnnotation": MetatranscriptomeAnnotation,
+        "nmdc:MetatranscriptomeAssembly": MetatranscriptomeAssembly,
+        "nmdc:MetatranscriptomeExpressionAnalysis": MetatranscriptomeExpressionAnalysis,
+        "nmdc:NucleotideSequencing": NucleotideSequencing,
+        "nmdc:ReadBasedTaxonomyAnalysis": ReadBasedTaxonomyAnalysis,
+        "nmdc:ReadQcAnalysis": ReadQcAnalysis,
+    }
+    record = _normalize_record(record)
+    target_class = record["type"].split(":")[1]
+    if validate:
+        validation_report = linkml.validator.validate(record, nmdc_materialized, target_class)
+        if validation_report.results:
+            raise ValueError(f"Validation error: {validation_report.results[0].message}")
+
+
+
+
+    try:
+        cls = process_types[record["type"]]
+    except KeyError:
+        raise ValueError(f"Invalid workflow execution type: {record['type']}")
+    wfe = cls(**record)
+    return wfe
+
+
+def _normalize_record(record: Dict[str, Any]) -> Dict[str, Any]:
+    """ Normalize the record by removing the _id field and converting the type field to a string """
+    record.pop("_id", None)
+    # for backwards compatibility strip Activity from the end of the type
+    record["type"] = record["type"].replace("Activity", "")
+    normalized_record = _strip_empty_values(record)
+
+
+    # type-specific normalization
+    if normalized_record["type"] == "nmdc:MagsAnalysis":
+        normalized_record = _normalize_mags_record(normalized_record)
+
+    return normalized_record
+
+
+def _normalize_mags_record(record: Dict[str, Any]) -> Dict[str, Any]:
+    """ Normalize the record for a MagsAnalysis object """
+    for i, mag in enumerate(record.get("mags_list", [])):
+        if not mag.get("type"):
+            # Update the original dictionary in the list
+            record["mags_list"][i]["type"] = "nmdc:MagBin"
+        # for backwards compatibility normalize num_tRNA to num_t_rna
+        if "num_tRNA" in mag:
+            record["mags_list"][i]["num_t_rna"] = mag.pop("num_tRNA")
+        # add type to eukaryotic_evaluation if it exists
+        if "eukaryotic_evaluation" in mag:
+            record["mags_list"][i]["eukaryotic_evaluation"]["type"] = "nmdc:EukEval"
+        # gene count should be a positive integer - remove if 'null'
+        if "gene_count" in mag and mag["gene_count"] == "null":
+            mag.pop("gene_count")
+    return record
+
+
+def _strip_empty_values(d: Dict[str, Any]) -> Dict[str, Any]:
+    """ Strip empty values from a record """
+    empty_values = [None, "", []]
+    def clean_dict(d):
+        if isinstance(d, dict):
+            return {k: clean_dict(v) for k, v in d.items() if v not in empty_values}
+        elif isinstance(d, list):
+            return [clean_dict(v) for v in d if v not in empty_values]
+        return d
+    return clean_dict(d)
+
+
+class DataObject(nmdc.DataObject):
+    """
+    Extends the NMDC DataObject dataclass with additional methods for serialization.
+    """
+    def __init__(self, **record):
+        """ Initialize the object from a dictionary """
+        # _id is a MongoDB field that makes the parent class fail to initialize
+        record.pop("_id", None)
+        if "type" not in record:
+            record["type"] = "nmdc:DataObject"
+        super().__init__(**record)
+
+    def as_dict(self) -> Dict[str, Any]:
+        """ Convert the object to a dictionary """
+        return yaml.safe_load(yaml_dumper.dumps(self))
diff --git a/nmdc_automation/workflow_automation/models.py b/nmdc_automation/models/workflow.py
similarity index 55%
rename from nmdc_automation/workflow_automation/models.py
rename to nmdc_automation/models/workflow.py
index 0db245ab..ed0b29f3 100644
--- a/nmdc_automation/workflow_automation/models.py
+++ b/nmdc_automation/models/workflow.py
@@ -1,90 +1,11 @@
-""" Model classes for the workflow automation app. """
+""" Data classed for NMDC workflow automation. """
 from dataclasses import dataclass, field
-from dateutil import parser
 from datetime import datetime
-from typing import List, Dict, Any, Optional, Set, Union
-
-from nmdc_schema.nmdc import (
-    DataGeneration,
-    FileTypeEnum,
-    NucleotideSequencing,
-    MagsAnalysis,
-    MetagenomeAssembly,
-    MetagenomeAnnotation,
-    MetatranscriptomeAssembly,
-    MetatranscriptomeAnnotation,
-    MetatranscriptomeExpressionAnalysis,
-    ReadBasedTaxonomyAnalysis,
-    ReadQcAnalysis,
-    WorkflowExecution
-)
-from nmdc_schema import nmdc
-
-
-def workflow_process_factory(record: Dict[str, Any]) -> Union[DataGeneration, WorkflowExecution]:
-    """
-    Factory function to create a PlannedProcess subclass object from a record.
-    Subclasses are determined by the "type" field in the record, and can be
-    either a WorkflowExecution or DataGeneration object.
-    """
-    process_types = {
-        "nmdc:MagsAnalysis": MagsAnalysis,
-        "nmdc:MetagenomeAnnotation": MetagenomeAnnotation,
-        "nmdc:MetagenomeAssembly": MetagenomeAssembly,
-        "nmdc:MetatranscriptomeAnnotation": MetatranscriptomeAnnotation,
-        "nmdc:MetatranscriptomeAssembly": MetatranscriptomeAssembly,
-        "nmdc:MetatranscriptomeExpressionAnalysis": MetatranscriptomeExpressionAnalysis,
-        "nmdc:NucleotideSequencing": NucleotideSequencing,
-        "nmdc:ReadBasedTaxonomyAnalysis": ReadBasedTaxonomyAnalysis,
-        "nmdc:ReadQcAnalysis": ReadQcAnalysis,
-    }
-    record = _normalize_record(record)
-
-    try:
-        cls = process_types[record["type"]]
-    except KeyError:
-        raise ValueError(f"Invalid workflow execution type: {record['type']}")
-    wfe = cls(**record)
-    return wfe
-
-def _normalize_record(record: Dict[str, Any]) -> Dict[str, Any]:
-    """ Normalize the record by removing the _id field and converting the type field to a string """
-    record.pop("_id", None)
-    # for backwards compatibility strip Activity from the end of the type
-    record["type"] = record["type"].replace("Activity", "")
-    normalized_record = _strip_empty_values(record)
-
-    # type-specific normalization
-    if normalized_record["type"] == "nmdc:MagsAnalysis":
-        normalized_record = _normalize_mags_record(normalized_record)
-
-    return normalized_record
-
-def _normalize_mags_record(record: Dict[str, Any]) -> Dict[str, Any]:
-    """ Normalize the record for a MagsAnalysis object """
-    for i, mag in enumerate(record.get("mags_list", [])):
-        if not mag.get("type"):
-            # Update the original dictionary in the list
-            record["mags_list"][i]["type"] = "nmdc:MagBin"
-        # for backwards compatibility normalize num_tRNA to num_t_rna
-        if "num_tRNA" in mag:
-            record["mags_list"][i]["num_t_rna"] = mag.pop("num_tRNA")
-        # add type to eukaryotic_evaluation if it exists
-        if "eukaryotic_evaluation" in mag:
-            record["mags_list"][i]["eukaryotic_evaluation"]["type"] = "nmdc:EukEval"
-    return record
-
-
-def _strip_empty_values(d: Dict[str, Any]) -> Dict[str, Any]:
-    """ Strip empty values from a record """
-    empty_values = [None, "", [], "null", 0]
-    def clean_dict(d):
-        if isinstance(d, dict):
-            return {k: clean_dict(v) for k, v in d.items() if v not in empty_values}
-        elif isinstance(d, list):
-            return [clean_dict(v) for v in d if v not in empty_values]
-        return d
-    return clean_dict(d)
+from typing import Any, Dict, List, Optional, Set
+
+from dateutil import parser
+
+from nmdc_automation.models.nmdc import DataObject, workflow_process_factory
 
 
 class WorkflowProcessNode(object):
@@ -108,7 +29,7 @@ def __eq__(self, other):
         return self.id == other.id and self.type == other.type
 
     def add_data_object(self, data_object):
-        self.data_objects_by_type[data_object.data_object_type] = data_object
+        self.data_objects_by_type[data_object.data_object_type.code.text] = data_object
 
     @property
     def id(self):
@@ -151,42 +72,6 @@ def was_informed_by(self):
         return getattr(self.process, "was_informed_by", self.id)
 
 
-class DataObject(nmdc.DataObject):
-    """
-    Extends the NMDC DataObject dataclass with additional methods for serialization.
-    """
-    def __init__(self, **record):
-        """ Initialize the object from a dictionary """
-        # _id is a MongoDB field that makes the parent class fail to initialize
-        record.pop("_id", None)
-        if "type" not in record:
-            record["type"] = "nmdc:DataObject"
-        super().__init__(**record)
-
-    def as_dict(self):
-        """ Return the object as a dictionary, excluding None values, empty lists, and data_object_type as a string """
-        return {
-            key: value
-            for key, value in self.__dict__.items()
-            if not key.startswith("_") and value
-        } | {"data_object_type": self.data_object_type}
-
-    @property
-    def data_object_type(self):
-        """ Return the data object type as a string """
-        if isinstance(self._data_object_type, FileTypeEnum):
-            return self._data_object_type.code.text
-        return str(self._data_object_type)
-
-    @data_object_type.setter
-    def data_object_type(self, value):
-        """ Set the data object type from a string or FileTypeEnum """
-        if isinstance(value, FileTypeEnum):
-            self._data_object_type = value
-        else:
-            self._data_object_type = FileTypeEnum(value)
-
-
 @dataclass
 class WorkflowConfig:
     """ Configuration for a workflow execution. Defined by .yaml files in nmdc_automation/config/workflows """
@@ -248,6 +133,7 @@ def add_parent(self, parent: "WorkflowConfig"):
 class JobWorkflow:
     id: str
 
+
 @dataclass
 class JobConfig:
     """ Represents a job configuration from the NMDC API jobs endpoint / MongoDB jobs collection """
@@ -271,6 +157,7 @@ class JobClaim:
     op_id: str
     site_id: str
 
+
 @dataclass
 class JobOutput:
     """ Represents a job output specification. """
@@ -292,6 +179,7 @@ def __post_init__(self):
             description=self.description,
         )
 
+
 @dataclass
 class Job:
     """ Represents a job from the NMDC API jobs endpoint / MongoDB jobs collection """
diff --git a/nmdc_automation/run_process/run_import.py b/nmdc_automation/run_process/run_import.py
index 2b4beb17..922765d3 100644
--- a/nmdc_automation/run_process/run_import.py
+++ b/nmdc_automation/run_process/run_import.py
@@ -1,8 +1,19 @@
 import click
-from typing import List
 import csv
+import importlib.resources
+from functools import lru_cache
+import logging
 import os
+import linkml.validator
+from linkml_runtime.dumpers import yaml_dumper
+import yaml
+
 from nmdc_automation.import_automation import GoldMapper
+from nmdc_automation.api import NmdcRuntimeApi
+
+
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
 
 
 @click.group()
@@ -15,34 +26,90 @@ def cli():
 @click.argument("import_yaml", type=click.Path(exists=True))
 @click.argument("site_configuration", type=click.Path(exists=True))
 @click.option("--iteration", default=1, type=str, help="Number of iterations")
-def project_import(import_file, import_yaml, site_configuration, iteration):
-    with open(import_file) as bioscales_file:
-        mappings = csv.reader(bioscales_file, delimiter="\t")
-
-        for line in mappings:
-            omics_processing_id = line[0]
-            project_path = line[3]
-            files_list = [
-                os.path.join(project_path, f)
-                for f in os.listdir(os.path.abspath(project_path))
-                if os.path.isfile(os.path.join(project_path, f))
-            ]
-
-            gold_mappings = GoldMapper(
-                iteration,
-                files_list,
-                omics_processing_id,
-                import_yaml,
-                project_path,
-                site_configuration,
-            )
-
-            gold_mappings.unique_object_mapper()
-            # gold_mappings.multiple_objects_mapper()
-            gold_mappings.activity_mapper()
-            response = gold_mappings.post_nmdc_database_object()
-            print(response)
-            print(f"processed {omics_processing_id}")
+def import_projects(import_file, import_yaml, site_configuration, iteration):
+
+    logger.info(f"Importing project from {import_file}")
+
+    runtime = NmdcRuntimeApi(site_configuration)
+    nmdc_materialized = _get_nmdc_materialized()
+
+    data_imports = _parse_tsv(import_file)
+    for data_import in data_imports:
+        project_path = data_import["project_path"]
+        nucleotide_sequencing_id = data_import["nucleotide_sequencing_id"]
+        files_list = [
+            os.path.join(project_path, f)
+            for f in os.listdir(os.path.abspath(project_path))
+            if os.path.isfile(os.path.join(project_path, f))
+        ]
+
+        logger.info(f"Importing {nucleotide_sequencing_id} from {project_path}: {len(files_list)} files")
+        mapper = GoldMapper(
+            iteration,
+            files_list,
+            nucleotide_sequencing_id,
+            import_yaml,
+            project_path,
+            runtime,
+        )
+        # Initialize the db with the sequencing data and create an update to be applied
+        # to the sequencing data generation has_output list
+        logger.info("Mapping sequencing data")
+        db, data_generation_update = mapper.map_sequencing_data()
+        # Map the rest of the data files - single files
+        logger.info("Mapping single data files")
+        db, do_mapping = mapper.map_data(db)
+        # Map the rest of the data files - multiple files
+        logger.info("Mapping multiple data files")
+        db, do_mapping = mapper.map_data(db, unique=False)
+
+        # map the workflow executions
+        logger.info("Mapping workflow executions")
+        db = mapper.map_workflow_executions(db)
+
+        # validate the database
+        logger.info("Validating imported data")
+        db_dict = yaml.safe_load(yaml_dumper.dumps(db))
+        validation_report = linkml.validator.validate(db_dict, nmdc_materialized)
+        if validation_report.results:
+            logger.error(f"Validation Failed")
+            for result in validation_report.results:
+                logger.error(result.message)
+            raise Exception("Validation Failed")
+        else:
+            logger.info("Validation Passed")
+
+        # apply the update to the sequencing data generation has_output list
+        logger.info("Applying update to sequencing data generation")
+        try:
+            runtime.run_query(data_generation_update)
+        except Exception as e:
+            logger.error(f"Error applying update to sequencing data generation: {e}")
+            raise e
+
+
+        # Post the data to the API
+        logger.info("Posting data to the API")
+        try:
+            runtime.post_objects(db_dict)
+        except Exception as e:
+            logger.error(f"Error posting data to the API: {e}")
+            raise e
+
+
+
+
+@lru_cache(maxsize=None)
+def _get_nmdc_materialized():
+    with importlib.resources.open_text("nmdc_schema", "nmdc_materialized_patterns.yaml") as f:
+        return yaml.safe_load(f)
+
+def _parse_tsv(file):
+    with open(file) as f:
+        reader = csv.DictReader(f, delimiter="\t")
+        data = [row for row in reader]
+
+    return data
 
 
 if __name__ == "__main__":
diff --git a/nmdc_automation/workflow_automation/sched.py b/nmdc_automation/workflow_automation/sched.py
index 08540658..8ddf92d5 100644
--- a/nmdc_automation/workflow_automation/sched.py
+++ b/nmdc_automation/workflow_automation/sched.py
@@ -10,7 +10,7 @@
 from pymongo import MongoClient
 from pymongo.database import Database as MongoDatabase
 from nmdc_automation.workflow_automation.workflow_process import load_workflow_process_nodes
-from nmdc_automation.workflow_automation.models import WorkflowProcessNode, WorkflowConfig
+from nmdc_automation.models.workflow import WorkflowConfig, WorkflowProcessNode
 from semver.version import Version
 
 
diff --git a/nmdc_automation/workflow_automation/watch_nmdc.py b/nmdc_automation/workflow_automation/watch_nmdc.py
index 5894df91..091b87aa 100644
--- a/nmdc_automation/workflow_automation/watch_nmdc.py
+++ b/nmdc_automation/workflow_automation/watch_nmdc.py
@@ -12,8 +12,7 @@
 from nmdc_schema.nmdc import Database
 from nmdc_automation.api import NmdcRuntimeApi
 from nmdc_automation.config import SiteConfig
-from .wfutils import WorkflowJob
-from .wfutils import  _md5
+from nmdc_automation.workflow_automation.wfutils import WorkflowJob
 
 
 DEFAULT_STATE_DIR = Path(__file__).parent / "_state"
diff --git a/nmdc_automation/workflow_automation/wfutils.py b/nmdc_automation/workflow_automation/wfutils.py
index 86c67912..a4f531e1 100755
--- a/nmdc_automation/workflow_automation/wfutils.py
+++ b/nmdc_automation/workflow_automation/wfutils.py
@@ -16,7 +16,7 @@
 import requests
 
 from nmdc_automation.config import SiteConfig
-from nmdc_automation.workflow_automation.models import DataObject
+from nmdc_automation.models.nmdc import DataObject
 
 DEFAULT_MAX_RETRIES = 2
 
diff --git a/nmdc_automation/workflow_automation/workflow_process.py b/nmdc_automation/workflow_automation/workflow_process.py
index 1e2b5382..194ac1a6 100644
--- a/nmdc_automation/workflow_automation/workflow_process.py
+++ b/nmdc_automation/workflow_automation/workflow_process.py
@@ -5,7 +5,8 @@
 
 from semver.version import Version
 
-from nmdc_automation.workflow_automation.models import WorkflowProcessNode, DataObject, WorkflowConfig
+from nmdc_automation.models.nmdc import DataObject
+from nmdc_automation.models.workflow import WorkflowConfig, WorkflowProcessNode
 
 warned_objects = set()
 
@@ -27,7 +28,7 @@ def get_required_data_objects_map(db, workflows: List[WorkflowConfig]) -> Dict[s
     required_data_objs_by_id = dict()
     for rec in db.data_object_set.find():
         do = DataObject(**rec)
-        if do.data_object_type not in required_types:
+        if do.data_object_type.code.text not in required_types:
             continue
         required_data_objs_by_id[do.id] = do
     return required_data_objs_by_id
@@ -64,7 +65,7 @@ def _check(match_types, data_object_ids, data_objs):
     do_types = set()
     for doid in data_object_ids:
         if doid in data_objs:
-            do_types.add(data_objs[doid].data_object_type)
+            do_types.add(data_objs[doid].data_object_type.code.text)
     return match_set.issubset(do_types)
 
 
diff --git a/nmdc_automation/workflow_automation/workflows.py b/nmdc_automation/workflow_automation/workflows.py
index acefd44b..f99cb4ee 100644
--- a/nmdc_automation/workflow_automation/workflows.py
+++ b/nmdc_automation/workflow_automation/workflows.py
@@ -5,7 +5,7 @@
 except ImportError:
     from yaml import Loader
 
-from nmdc_automation.workflow_automation.models import WorkflowConfig
+from nmdc_automation.models.workflow import WorkflowConfig
 
 
 def load_workflow_configs(yaml_file) -> list[WorkflowConfig]:
diff --git a/poetry.lock b/poetry.lock
index f71e5de7..c88772a5 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -131,101 +131,116 @@ files = [
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
-    {file = "charset-normalizer-3.3.2.tar.gz", hash = "sha256:f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:25baf083bf6f6b341f4121c2f3c548875ee6f5339300e08be3f2b2ba1721cdd3"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:06435b539f889b1f6f4ac1758871aae42dc3a8c0e24ac9e60c2384973ad73027"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9063e24fdb1e498ab71cb7419e24622516c4a04476b17a2dab57e8baa30d6e03"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:6897af51655e3691ff853668779c7bad41579facacf5fd7253b0133308cf000d"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_ppc64le.manylinux2014_ppc64le.whl", hash = "sha256:1d3193f4a680c64b4b6a9115943538edb896edc190f0b222e73761716519268e"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_s390x.manylinux2014_s390x.whl", hash = "sha256:cd70574b12bb8a4d2aaa0094515df2463cb429d8536cfb6c7ce983246983e5a6"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:8465322196c8b4d7ab6d1e049e4c5cb460d0394da4a27d23cc242fbf0034b6b5"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-manylinux_2_5_i686.manylinux1_i686.manylinux_2_17_i686.manylinux2014_i686.whl", hash = "sha256:a9a8e9031d613fd2009c182b69c7b2c1ef8239a0efb1df3f7c8da66d5dd3d537"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_aarch64.whl", hash = "sha256:beb58fe5cdb101e3a055192ac291b7a21e3b7ef4f67fa1d74e331a7f2124341c"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:e06ed3eb3218bc64786f7db41917d4e686cc4856944f53d5bdf83a6884432e12"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_ppc64le.whl", hash = "sha256:2e81c7b9c8979ce92ed306c249d46894776a909505d8f5a4ba55b14206e3222f"},
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-    {file = "charset_normalizer-3.3.2-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:fd1abc0d89e30cc4e02e4064dc67fcc51bd941eb395c502aac3ec19fab46b519"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-win32.whl", hash = "sha256:3d47fa203a7bd9c5b6cee4736ee84ca03b8ef23193c0d1ca99b5089f72645c73"},
-    {file = "charset_normalizer-3.3.2-cp310-cp310-win_amd64.whl", hash = "sha256:10955842570876604d404661fbccbc9c7e684caf432c09c715ec38fbae45ae09"},
-    {file = "charset_normalizer-3.3.2-cp311-cp311-macosx_10_9_universal2.whl", hash = "sha256:802fe99cca7457642125a8a88a084cef28ff0cf9407060f7b93dca5aa25480db"},
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 ]
 
 [package.dependencies]
@@ -611,6 +616,23 @@ files = [
     {file = "hbreader-0.9.1.tar.gz", hash = "sha256:d2c132f8ba6276d794c66224c3297cec25c8079d0a4cf019c061611e0a3b94fa"},
 ]
 
+[[package]]
+name = "html5lib-modern"
+version = "1.2"
+description = "HTML parser based on the WHATWG HTML specification"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "html5lib_modern-1.2-py2.py3-none-any.whl", hash = "sha256:3458b6e31525ede4fcaac0ff42d9eeb5efaf755473768103cb56e0275caa8d99"},
+    {file = "html5lib_modern-1.2.tar.gz", hash = "sha256:1fadbfc27ea955431270e4e79a4a4c290ba11c3a3098a95cc22dc73e312a1768"},
+]
+
+[package.extras]
+all = ["chardet (>=2.2.1)", "genshi (>=0.7.1)", "lxml (>=3.4.0)"]
+chardet = ["chardet (>=2.2.1)"]
+genshi = ["genshi (>=0.7.1)"]
+lxml = ["lxml (>=3.4.0)"]
+
 [[package]]
 name = "idna"
 version = "3.10"
@@ -625,6 +647,16 @@ files = [
 [package.extras]
 all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2)"]
 
+[[package]]
+name = "importlib"
+version = "1.0.4"
+description = "Backport of importlib.import_module() from Python 2.7"
+optional = false
+python-versions = "*"
+files = [
+    {file = "importlib-1.0.4.zip", hash = "sha256:b6ee7066fea66e35f8d0acee24d98006de1a0a8a94a8ce6efe73a9a23c8d9826"},
+]
+
 [[package]]
 name = "importlib-metadata"
 version = "8.5.0"
@@ -661,18 +693,15 @@ files = [
 
 [[package]]
 name = "isodate"
-version = "0.6.1"
+version = "0.7.2"
 description = "An ISO 8601 date/time/duration parser and formatter"
 optional = false
-python-versions = "*"
+python-versions = ">=3.7"
 files = [
-    {file = "isodate-0.6.1-py2.py3-none-any.whl", hash = "sha256:0751eece944162659049d35f4f549ed815792b38793f07cf73381c1c87cbed96"},
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+    {file = "isodate-0.7.2.tar.gz", hash = "sha256:4cd1aa0f43ca76f4a6c6c0292a85f40b35ec2e43e315b59f06e6d32171a953e6"},
 ]
 
-[package.dependencies]
-six = "*"
-
 [[package]]
 name = "isoduration"
 version = "20.11.0"
@@ -774,13 +803,12 @@ jsonpointer = ">=1.9"
 
 [[package]]
 name = "jsonpath-ng"
-version = "1.6.1"
+version = "1.7.0"
 description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
 optional = false
 python-versions = "*"
 files = [
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+    {file = "jsonpath-ng-1.7.0.tar.gz", hash = "sha256:f6f5f7fd4e5ff79c785f1573b394043b39849fb2bb47bcead935d12b00beab3c"},
 ]
 
 [package.dependencies]
@@ -1087,13 +1115,13 @@ pyyaml = ">=5.1"
 
 [[package]]
 name = "mkdocs-material"
-version = "9.5.39"
+version = "9.5.41"
 description = "Documentation that simply works"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "mkdocs_material-9.5.39-py3-none-any.whl", hash = "sha256:0f2f68c8db89523cb4a59705cd01b4acd62b2f71218ccb67e1e004e560410d2b"},
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+    {file = "mkdocs_material-9.5.41-py3-none-any.whl", hash = "sha256:990bc138c33342b5b73e7545915ebc0136e501bfbd8e365735144f5120891d83"},
+    {file = "mkdocs_material-9.5.41.tar.gz", hash = "sha256:30fa5d459b4b8130848ecd8e1c908878345d9d8268f7ddbc31eebe88d462d97b"},
 ]
 
 [package.dependencies]
@@ -1186,13 +1214,13 @@ pymongo = ["pymongo"]
 
 [[package]]
 name = "nmdc-schema"
-version = "11.0.1"
+version = "11.0.3"
 description = "Schema resources for the National Microbiome Data Collaborative (NMDC)"
 optional = false
 python-versions = "<4.0,>=3.9"
 files = [
-    {file = "nmdc_schema-11.0.1-py3-none-any.whl", hash = "sha256:ff4e8a150fd192fb8daf7423f7ac1bd6b0dd26c68d8030e0359748fbf4e8fd15"},
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+    {file = "nmdc_schema-11.0.3-py3-none-any.whl", hash = "sha256:e2b6bc44382c75b2522d6da2767e802a970dcc0de8db9b90aeede82769884703"},
+    {file = "nmdc_schema-11.0.3.tar.gz", hash = "sha256:679ce7817766673a3bf08dfd2bd2b6a348c7fb6e6a0a742cce8cdd53a4bda8ca"},
 ]
 
 [package.dependencies]
@@ -1546,13 +1574,13 @@ requests = ">=2.28.1,<3.0.0"
 
 [[package]]
 name = "prefixmaps"
-version = "0.2.5"
+version = "0.2.6"
 description = "A python library for retrieving semantic prefix maps"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "prefixmaps-0.2.5-py3-none-any.whl", hash = "sha256:68caa04b3a6a8e058aa1c55affe32c62e44b564d031d63f768e267b796a1f3ee"},
-    {file = "prefixmaps-0.2.5.tar.gz", hash = "sha256:aaccd2425ade2ea97a502c58be49fe8f3536e3d5e919712ae0358a39fc800799"},
+    {file = "prefixmaps-0.2.6-py3-none-any.whl", hash = "sha256:f6cef28a7320fc6337cf411be212948ce570333a0ce958940ef684c7fb192a62"},
+    {file = "prefixmaps-0.2.6.tar.gz", hash = "sha256:7421e1244eea610217fa1ba96c9aebd64e8162a930dc0626207cd8bf62ecf4b9"},
 ]
 
 [package.dependencies]
@@ -1835,13 +1863,13 @@ zstd = ["zstandard"]
 
 [[package]]
 name = "pyparsing"
-version = "3.1.4"
+version = "3.2.0"
 description = "pyparsing module - Classes and methods to define and execute parsing grammars"
 optional = false
-python-versions = ">=3.6.8"
+python-versions = ">=3.9"
 files = [
-    {file = "pyparsing-3.1.4-py3-none-any.whl", hash = "sha256:a6a7ee4235a3f944aa1fa2249307708f893fe5717dc603503c6c7969c070fb7c"},
-    {file = "pyparsing-3.1.4.tar.gz", hash = "sha256:f86ec8d1a83f11977c9a6ea7598e8c27fc5cddfa5b07ea2241edbbde1d7bc032"},
+    {file = "pyparsing-3.2.0-py3-none-any.whl", hash = "sha256:93d9577b88da0bbea8cc8334ee8b918ed014968fd2ec383e868fb8afb1ccef84"},
+    {file = "pyparsing-3.2.0.tar.gz", hash = "sha256:cbf74e27246d595d9a74b186b810f6fbb86726dbf3b9532efb343f6d7294fe9c"},
 ]
 
 [package.extras]
@@ -2169,24 +2197,25 @@ pyyaml = "*"
 
 [[package]]
 name = "rdflib"
-version = "7.0.0"
+version = "7.1.0"
 description = "RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information."
 optional = false
-python-versions = ">=3.8.1,<4.0.0"
+python-versions = "<4.0.0,>=3.8.1"
 files = [
-    {file = "rdflib-7.0.0-py3-none-any.whl", hash = "sha256:0438920912a642c866a513de6fe8a0001bd86ef975057d6962c79ce4771687cd"},
-    {file = "rdflib-7.0.0.tar.gz", hash = "sha256:9995eb8569428059b8c1affd26b25eac510d64f5043d9ce8c84e0d0036e995ae"},
+    {file = "rdflib-7.1.0-py3-none-any.whl", hash = "sha256:240c25c6e1b573ffa67aed23aae128e253c443c15291c9a01d8d392ea80c05b6"},
+    {file = "rdflib-7.1.0.tar.gz", hash = "sha256:a29a8fccebd3d3a5f1b7e88d92dace1c89829018c7d29a6114fff4449c188b3b"},
 ]
 
 [package.dependencies]
-isodate = ">=0.6.0,<0.7.0"
+html5lib-modern = ">=1.2,<2.0"
+isodate = {version = ">=0.7.2,<1.0.0", markers = "python_version < \"3.11\""}
 pyparsing = ">=2.1.0,<4"
 
 [package.extras]
 berkeleydb = ["berkeleydb (>=18.1.0,<19.0.0)"]
-html = ["html5lib (>=1.0,<2.0)"]
-lxml = ["lxml (>=4.3.0,<5.0.0)"]
-networkx = ["networkx (>=2.0.0,<3.0.0)"]
+lxml = ["lxml (>=4.3,<6.0)"]
+networkx = ["networkx (>=2,<4)"]
+orjson = ["orjson (>=3.9.14,<4)"]
 
 [[package]]
 name = "rdflib-jsonld"
@@ -2537,24 +2566,24 @@ python-versions = ">=3.6"
 files = [
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+    {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-manylinux2014_aarch64.whl", hash = "sha256:d92f81886165cb14d7b067ef37e142256f1c6a90a65cd156b063a43da1708cfd"},
     {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:fff3573c2db359f091e1589c3d7c5fc2f86f5bdb6f24252c2d8e539d4e45f412"},
-    {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-manylinux_2_24_aarch64.whl", hash = "sha256:aa2267c6a303eb483de8d02db2871afb5c5fc15618d894300b88958f729ad74f"},
     {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-musllinux_1_1_i686.whl", hash = "sha256:840f0c7f194986a63d2c2465ca63af8ccbbc90ab1c6001b1978f05119b5e7334"},
     {file = "ruamel.yaml.clib-0.2.8-cp310-cp310-musllinux_1_1_x86_64.whl", hash = "sha256:024cfe1fc7c7f4e1aff4a81e718109e13409767e4f871443cbff3dba3578203d"},
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+    {file = "sqlalchemy-2.0.36.tar.gz", hash = "sha256:7f2767680b6d2398aea7082e45a774b2b0767b5c8d8ffb9c8b683088ea9b29c5"},
 ]
 
 [package.dependencies]
@@ -2775,7 +2812,7 @@ aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
 aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5,!=1.1.10)"]
 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
@@ -3027,4 +3064,4 @@ type = ["pytest-mypy"]
 [metadata]
 lock-version = "2.0"
 python-versions = "^3.9"
-content-hash = "66d85f7aabd3fae397f61f071a2f4e5ea0361eba5fe846213e9b5e6bcdc759c7"
+content-hash = "abe523d5df94ecbf819e7c5f08721410df1e77dabd1739f80d0ea6c97b284a08"
diff --git a/pyproject.toml b/pyproject.toml
index 51c545b2..653dae6a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -12,7 +12,7 @@ python = "^3.9"
 pymongo = "^4.3.3"
 pyYAML = "^6.0"
 requests = "^2.28.2"
-nmdc-schema = "^11.0.1"
+nmdc-schema = "^11.0.3"
 deepdiff = "^6.2.1"
 pytz = "^2023.3"
 python-dotenv = "^1.0.0"
@@ -28,6 +28,7 @@ mongomock = "^4.1.2"
 requests-mock = "^1.11.0"
 pytest-local-badge = "^1.0.3"
 pysam = "^0.22.1"
+importlib = "^1.0.4"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.3.1"
diff --git a/tests/conftest.py b/tests/conftest.py
index b8a89714..b14164d5 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -6,12 +6,12 @@
 import requests_mock
 import shutil
 from time import time
-from unittest.mock import Mock
+from unittest.mock import MagicMock
 from yaml import load, Loader
 
 
 from nmdc_automation.config import SiteConfig
-from nmdc_automation.workflow_automation.models import WorkflowConfig
+from nmdc_automation.models.workflow import WorkflowConfig
 from tests.fixtures import db_utils
 from nmdc_automation.workflow_automation.wfutils import WorkflowJob
 
@@ -22,6 +22,36 @@ def mock_job_state():
     )
     return state
 
+@fixture(scope="session")
+def mock_nucleotide_sequencing():
+    return {
+        "id": "nmdc:omprc-11-metag1",
+        "name": "Test Metagenome Processing",
+        "has_input": [
+            "nmdc:bsm-11-qezc0h51"
+        ],
+        "has_output": [
+            "nmdc:dobj-11-rawreads1",
+            "nmdc:dobj-11-rawreads2"
+        ],
+        "analyte_category": "metagenome",
+        "associated_studies": [
+            "nmdc:sty-11-test001"
+        ],
+        "processing_institution": "JGI",
+        "principal_investigator": {
+            "has_raw_value": "PI Name",
+            "email": "pi_name@example.com",
+            "name": "PI Name",
+            "type": "nmdc:PersonValue"
+        },
+        "type": "nmdc:NucleotideSequencing"
+    }
+
+
+@fixture(scope="session")
+def mock_metagenome_assembly():
+    return
 
 @fixture(scope="session")
 def mags_config(fixtures_dir)->WorkflowConfig:
@@ -46,7 +76,9 @@ def mock_api(monkeypatch, requests_mock, test_data_dir):
             "access_token": "abcd"
             }
     requests_mock.post("http://localhost/token", json=token_resp)
-    resp = ["nmdc:abcd"]
+    resp = ["nmdc:dobj-01-abcd4321"]
+    # mock mint responses in sequence
+
     requests_mock.post("http://localhost/pids/mint", json=resp)
     requests_mock.post(
         "http://localhost/workflows/workflow_executions",
@@ -156,4 +188,60 @@ def mock_cromwell_api(fixtures_dir):
             json=successful_job_metadata
             )
 
-        yield m
\ No newline at end of file
+        yield m
+
+
+@fixture(scope="session")
+def gold_import_dir(fixtures_dir):
+    return fixtures_dir / "gold_import"
+
+@fixture(scope="session")
+def gold_import_files(gold_import_dir):
+    # return the full paths to fixtures that simulate JGI import files. These are used to test the GoldMapper class.
+    # One (1) file is a nucleotide sequencing file. All the other files are RQC, assembly, MAGs, etc.
+    return [str(f) for f in gold_import_dir.iterdir() if f.is_file()]
+
+
+class MockNmdcRuntimeApi:
+    def __init__(self):
+        self.counter = 10
+
+    def minter(self, id_type):
+        type_code_map = {
+            "nmdc:DataObject": "nmdc:dobj",
+            "nmdc:MetagenomeAssembly": "nmdc:wfmgas",
+            "nmdc:MetagenomeAnnotation": "nmdc:wfmgan",
+            "nmdc:MagsAnalysis": "nmdc:wfmag",
+            "nmdc:ReadQcAnalysis": "nmdc:wfrqc",
+            "nmdc:ReadBasedTaxonomyAnalysis": "nmdc:wfrbt",
+        }
+        self.counter += 1
+        prefix = type_code_map[id_type]
+        return f"{prefix}-{self.counter:02d}-abcd1234"
+
+    def get_token(self):
+        return {"expires": {"minutes": time()+60},
+            "access_token": "abcd"
+            }
+
+    def refresh_token(self):
+        return {"expires": {"minutes": time()+60},
+            "access_token": "abcd"
+            }
+
+    def get_object(self, id):
+        return {
+            "id": id,
+            "name": "Test Object",
+            "type": "nmdc:DataObject"
+        }
+
+
+
+
+
+
+
+@fixture(scope="session")
+def mock_nmdc_runtime_api():
+    return MockNmdcRuntimeApi()
diff --git a/tests/db_dict.json b/tests/db_dict.json
new file mode 100644
index 00000000..8c332851
--- /dev/null
+++ b/tests/db_dict.json
@@ -0,0 +1,136 @@
+{
+  "data_object_set": [
+    {
+      "id": "nmdc:dobj-11-abcd1234",
+      "type": "nmdc:DataObject",
+      "name": "52834.4.466476.GATCGAGT-GATCGAGT.fastq.gz",
+      "description": "Metagenome Raw Reads for nmdc:omprc-11-importT",
+      "data_object_type": "Metagenome Raw Reads",
+      "file_size_bytes": 114,
+      "md5_checksum": "d007b1a06373c7ae7c15e681b41a0fc3",
+      "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-importT/52834.4.466476.GATCGAGT-GATCGAGT.fastq.gz"
+    },
+    {
+      "id": "nmdc:dobj-13-abcd1234",
+      "type": "nmdc:DataObject",
+      "name": "nmdc_wfmgan-12-abcd1234.1_proteins.faa",
+      "description": "FASTA Amino Acid File for nmdc:omprc-11-importT",
+      "data_object_type": "Annotation Amino Acid FASTA",
+      "file_size_bytes": 675,
+      "md5_checksum": "272b6e22c3a418f3e2819e2485f3bf01",
+      "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-importT/nmdc:wfmgan-12-abcd1234.1/nmdc_wfmgan-12-abcd1234.1_proteins.faa"
+    },
+    {
+      "id": "nmdc:dobj-14-abcd1234",
+      "type": "nmdc:DataObject",
+      "name": "nmdc_wfmgan-12-abcd1234.1_cog.gff",
+      "description": "COGs for nmdc:omprc-11-importT",
+      "data_object_type": "Clusters of Orthologous Groups (COG) Annotation GFF",
+      "file_size_bytes": 2618,
+      "md5_checksum": "513be591318b13d46d318bc6bd2c859c",
+      "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-importT/nmdc:wfmgan-12-abcd1234.1/nmdc_wfmgan-12-abcd1234.1_cog.gff"
+    },
+    {
+      "id": "nmdc:dobj-15-abcd1234",
+      "type": "nmdc:DataObject",
+      "name": "nmdc_wfmgan-12-abcd1234.1_pfam.gff",
+      "description": "Pfam Annotation for nmdc:omprc-11-importT",
+      "data_object_type": "Pfam Annotation GFF",
+      "file_size_bytes": 0,
+      "md5_checksum": "d41d8cd98f00b204e9800998ecf8427e",
+      "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-importT/nmdc:wfmgan-12-abcd1234.1/nmdc_wfmgan-12-abcd1234.1_pfam.gff"
+    },
+    {
+      "id": "nmdc:dobj-17-abcd1234",
+      "type": "nmdc:DataObject",
+      "name": "nmdc_wfrqc-16-abcd1234.1_filtered.fastq.gz",
+      "description": "Reads QC for nmdc:omprc-11-importT",
+      "data_object_type": "Filtered Sequencing Reads",
+      "file_size_bytes": 114,
+      "md5_checksum": "d007b1a06373c7ae7c15e681b41a0fc3",
+      "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-importT/nmdc:wfrqc-16-abcd1234.1/nmdc_wfrqc-16-abcd1234.1_filtered.fastq.gz"
+    },
+    {
+      "id": "nmdc:dobj-19-abcd1234",
+      "type": "nmdc:DataObject",
+      "name": "nmdc_wfmgas-18-abcd1234.1_contigs.fna",
+      "description": "Assembly contigs for nmdc:omprc-11-importT",
+      "data_object_type": "Assembly Contigs",
+      "file_size_bytes": 563,
+      "md5_checksum": "a9838d4cb59f6444d63b5d254af9a479",
+      "url": "https://data.microbiomedata.org/data/nmdc:omprc-11-importT/nmdc:wfmgas-18-abcd1234.1/nmdc_wfmgas-18-abcd1234.1_contigs.fna"
+    }
+  ],
+  "workflow_execution_set": [
+    {
+      "id": "nmdc:wfrqc-16-abcd1234.1",
+      "type": "nmdc:ReadQcAnalysis",
+      "name": "Read QC for nmdc:wfrqc-16-abcd1234.1",
+      "has_input": [
+        "nmdc:dobj-11-abcd1234"
+      ],
+      "has_output": [
+        "nmdc:dobj-17-abcd1234"
+      ],
+      "execution_resource": "JGI",
+      "git_url": "https://github.com/microbiomedata/ReadsQC",
+      "started_at_time": "2024-10-18T15:36:13.791386+00:00",
+      "was_informed_by": "nmdc:omprc-11-importT",
+      "ended_at_time": "2024-10-18T15:36:13.791397+00:00",
+      "version": "v1.0.8"
+    },
+    {
+      "id": "nmdc:wfmgas-18-abcd1234.1",
+      "type": "nmdc:MetagenomeAssembly",
+      "name": "Metagenome Assembly for nmdc:wfmgas-18-abcd1234.1",
+      "has_input": [
+        "nmdc:dobj-17-abcd1234"
+      ],
+      "has_output": [
+        "nmdc:dobj-19-abcd1234"
+      ],
+      "execution_resource": "JGI",
+      "git_url": "https://github.com/microbiomedata/metaAssembly",
+      "started_at_time": "2024-10-18T15:36:17.489784+00:00",
+      "was_informed_by": "nmdc:omprc-11-importT",
+      "ended_at_time": "2024-10-18T15:36:17.489798+00:00",
+      "version": "v1.0.3"
+    },
+    {
+      "id": "nmdc:wfmgan-12-abcd1234.1",
+      "type": "nmdc:MetagenomeAnnotation",
+      "name": "Metagenome Annotation Analysis for nmdc:wfmgan-12-abcd1234.1",
+      "has_input": [
+        "nmdc:dobj-19-abcd1234"
+      ],
+      "has_output": [
+        "nmdc:dobj-13-abcd1234",
+        "nmdc:dobj-14-abcd1234",
+        "nmdc:dobj-15-abcd1234"
+      ],
+      "execution_resource": "JGI",
+      "git_url": "https://github.com/microbiomedata/mg_annotation",
+      "started_at_time": "2024-10-18T15:36:17.489960+00:00",
+      "was_informed_by": "nmdc:omprc-11-importT",
+      "ended_at_time": "2024-10-18T15:36:17.489965+00:00",
+      "version": "v1.0.4"
+    },
+    {
+      "id": "nmdc:wfmags-20-abcd1234.1",
+      "type": "nmdc:MagsAnalysis",
+      "name": "Metagenome Assembled Genomes Analysis for nmdc:wfmags-20-abcd1234.1",
+      "has_input": [
+        "nmdc:dobj-13-abcd1234",
+        "nmdc:dobj-14-abcd1234",
+        "nmdc:dobj-15-abcd1234",
+        "nmdc:dobj-19-abcd1234"
+      ],
+      "execution_resource": "JGI",
+      "git_url": "https://github.com/microbiomedata/metaMAGs",
+      "started_at_time": "2024-10-18T15:36:17.490112+00:00",
+      "was_informed_by": "nmdc:omprc-11-importT",
+      "ended_at_time": "2024-10-18T15:36:17.490117+00:00",
+      "version": "v1.0.6"
+    }
+  ]
+}
diff --git a/tests/fixtures/gold_import/52834.4.466476.GATCGAGT-GATCGAGT.fastq.gz b/tests/fixtures/gold_import/52834.4.466476.GATCGAGT-GATCGAGT.fastq.gz
new file mode 100644
index 00000000..8136bfd9
Binary files /dev/null and b/tests/fixtures/gold_import/52834.4.466476.GATCGAGT-GATCGAGT.fastq.gz differ
diff --git a/tests/fixtures/gold_import/52834.4.466476.GATCGAGT-GATCGAGT.filter-METAGENOME.fastq.gz b/tests/fixtures/gold_import/52834.4.466476.GATCGAGT-GATCGAGT.filter-METAGENOME.fastq.gz
new file mode 100644
index 00000000..8136bfd9
Binary files /dev/null and b/tests/fixtures/gold_import/52834.4.466476.GATCGAGT-GATCGAGT.filter-METAGENOME.fastq.gz differ
diff --git a/tests/fixtures/gold_import/assembly.contigs.fasta b/tests/fixtures/gold_import/assembly.contigs.fasta
new file mode 100644
index 00000000..12114f4e
--- /dev/null
+++ b/tests/fixtures/gold_import/assembly.contigs.fasta
@@ -0,0 +1,10 @@
+>scaffold_1_c2
+AAATTGGTGGCTAAGCCACCAATTTCCGCACAAAAACAACCTCTTTTCTAGTGGTAAGAC
+GTTTTGGCGACTTTGACACTGCCCTATTTTCCAGGTAATTGCCTATTGACAATGCATCCA
+TATGGATGTATAATCGGGTTACTTCAGATGTTGAGCTTTGGCTCTTTTTTGAAGTGACTG
+AACTCCGGTTGGTCCGCAAGGATTGCCTGGAGTTCTTTATTTATCCCCAGCCGGGACGTT
+GTTCCGGTTGGGGCTTCTTTTTTATCCGGGAACGCTGTAGAGCGGAAGGAGATAAAAGCC
+GTGTCGCAATTCGAGGCAAACCACGTGGAGAGAAGCGCAACCATCACCCTTGTGGCCCCA
+CCGGACAAGGTATTCCACCTGTTCGAGCCTATAGGAGAGAAAGCATGGGCGGCAGGCTGG
+GAGCCGCGCTTCGTGTACCCACAGGACGAGGAGGCTAAGGAGGGAGCCGTCTTCAAAATA
+GAGGCTGAAAACGGGCCGGACACGACCTGGATCATCAGCCGCTACGACAGGGAGCATAAC
\ No newline at end of file
diff --git a/tests/test_data/test_2.tar.gz b/tests/fixtures/gold_import/test_2.tar.gz
similarity index 100%
rename from tests/test_data/test_2.tar.gz
rename to tests/fixtures/gold_import/test_2.tar.gz
diff --git a/tests/test_data/test_72.tar.gz b/tests/fixtures/gold_import/test_72.tar.gz
similarity index 100%
rename from tests/test_data/test_72.tar.gz
rename to tests/fixtures/gold_import/test_72.tar.gz
diff --git a/tests/test_data/test_cog.gff b/tests/fixtures/gold_import/test_cog.gff
similarity index 100%
rename from tests/test_data/test_cog.gff
rename to tests/fixtures/gold_import/test_cog.gff
diff --git a/tests/test_data/test_pfam.gff b/tests/fixtures/gold_import/test_pfam.gff
similarity index 100%
rename from tests/test_data/test_pfam.gff
rename to tests/fixtures/gold_import/test_pfam.gff
diff --git a/tests/fixtures/gold_import/test_proteins.faa b/tests/fixtures/gold_import/test_proteins.faa
new file mode 100644
index 00000000..2bd968a4
--- /dev/null
+++ b/tests/fixtures/gold_import/test_proteins.faa
@@ -0,0 +1,10 @@
+>Ga0597026_0000001_301_783 # Prodigal v2.6.3_patched # 301 # 783 # + # tt=11
+MSQFEANHVERSATITLVAPPDKVFHLFEPIGEKAWAAGWEPRFVYPQDEEAKEGAVFKIEAENGPDTTW
+IISRYDREHNAIEYMTVKPDTRVGRIRVEVAGGSEGTSIAAVSYTFTALTEQGNALNDSFTEDHYRHKMH
+WWEKAINHYLRTGETLAHHD
+>Ga0597026_0000001_1887_3365 # Prodigal v2.6.3_patched # 1887 # 3365 # + # tt=11
+MIDQIRPRLEDNTLLRQLALVLLALGVGVAGGLAIVAGNPVVPFVALTGLLALPWLVTRPMADMLLVVCT
+ATLLPFAASPVRLAVLTPTLLEVGLLLLYMAWLLRMLLNTGEGFARTPVDVWVMLFLACTLFAFVLGLGR
+DASTDVVHNYFKMLLSIGVFFAAANVIRTWEQVATVLKALIVSGAAAASIGIVLWRLPDTFAASLLTRLS
+VIGYPTERVIRYVEENPALGERAVGTQVDPNSFAGMLVIIAAITGVHLLSRKPLLPRWLLAGMLLVDVAA
+IVLTQSRSALLGILVAAALVATLRYRHLWTWGVAGAVAIAVLGVGSGYFARLTAGIRFEDQASIMRLAEY
\ No newline at end of file
diff --git a/tests/fixtures/models/mags_analysis_record.json b/tests/fixtures/models/mags_analysis_record.json
index df222d83..34778ead 100644
--- a/tests/fixtures/models/mags_analysis_record.json
+++ b/tests/fixtures/models/mags_analysis_record.json
@@ -52,52 +52,7 @@
       "gtdbtk_family": "UBA11358",
       "gtdbtk_genus": "UBA11358",
       "gtdbtk_species": "null",
-      "members_id": [
-        "nmdc:wfmgas-13-56028x05.1_7_c1",
-        "nmdc:wfmgas-13-56028x05.1_9_c1",
-        "nmdc:wfmgas-13-56028x05.1_16_c1",
-        "nmdc:wfmgas-13-56028x05.1_20_c1",
-        "nmdc:wfmgas-13-56028x05.1_23_c1",
-        "nmdc:wfmgas-13-56028x05.1_27_c1",
-        "nmdc:wfmgas-13-56028x05.1_45_c1",
-        "nmdc:wfmgas-13-56028x05.1_55_c1",
-        "nmdc:wfmgas-13-56028x05.1_71_c1",
-        "nmdc:wfmgas-13-56028x05.1_79_c1",
-        "nmdc:wfmgas-13-56028x05.1_99_c1",
-        "nmdc:wfmgas-13-56028x05.1_52_c2",
-        "nmdc:wfmgas-13-56028x05.1_127_c1",
-        "nmdc:wfmgas-13-56028x05.1_131_c1",
-        "nmdc:wfmgas-13-56028x05.1_137_c1",
-        "nmdc:wfmgas-13-56028x05.1_169_c1",
-        "nmdc:wfmgas-13-56028x05.1_200_c1",
-        "nmdc:wfmgas-13-56028x05.1_212_c1",
-        "nmdc:wfmgas-13-56028x05.1_223_c1",
-        "nmdc:wfmgas-13-56028x05.1_372_c1",
-        "nmdc:wfmgas-13-56028x05.1_393_c1",
-        "nmdc:wfmgas-13-56028x05.1_428_c1",
-        "nmdc:wfmgas-13-56028x05.1_52_c1",
-        "nmdc:wfmgas-13-56028x05.1_582_c1",
-        "nmdc:wfmgas-13-56028x05.1_706_c1",
-        "nmdc:wfmgas-13-56028x05.1_888_c1",
-        "nmdc:wfmgas-13-56028x05.1_912_c1",
-        "nmdc:wfmgas-13-56028x05.1_1268_c1",
-        "nmdc:wfmgas-13-56028x05.1_1271_c1",
-        "nmdc:wfmgas-13-56028x05.1_1492_c1",
-        "nmdc:wfmgas-13-56028x05.1_1494_c1",
-        "nmdc:wfmgas-13-56028x05.1_1604_c1",
-        "nmdc:wfmgas-13-56028x05.1_1627_c1",
-        "nmdc:wfmgas-13-56028x05.1_1888_c1",
-        "nmdc:wfmgas-13-56028x05.1_1938_c1",
-        "nmdc:wfmgas-13-56028x05.1_2944_c1",
-        "nmdc:wfmgas-13-56028x05.1_3261_c1",
-        "nmdc:wfmgas-13-56028x05.1_3477_c1",
-        "nmdc:wfmgas-13-56028x05.1_4194_c1",
-        "nmdc:wfmgas-13-56028x05.1_6257_c1",
-        "nmdc:wfmgas-13-56028x05.1_7589_c1",
-        "nmdc:wfmgas-13-56028x05.1_10469_c1",
-        "nmdc:wfmgas-13-56028x05.1_10553_c1",
-        "nmdc:wfmgas-13-56028x05.1_13792_c1"
-      ]
+      "members_id": ["nmdc:wfmgas-13-56028x05.1_7_c1", "nmdc:wfmgas-13-56028x05.1_7_c2"]
     },
     {
       "bin_name": "bins.9",
@@ -118,100 +73,7 @@
       "gtdbtk_family": "null",
       "gtdbtk_genus": "null",
       "gtdbtk_species": "null",
-      "members_id": [
-        "nmdc:wfmgas-13-56028x05.1_7094_c1",
-        "nmdc:wfmgas-13-56028x05.1_9486_c1",
-        "nmdc:wfmgas-13-56028x05.1_9853_c1",
-        "nmdc:wfmgas-13-56028x05.1_10857_c1",
-        "nmdc:wfmgas-13-56028x05.1_11702_c1",
-        "nmdc:wfmgas-13-56028x05.1_12042_c1",
-        "nmdc:wfmgas-13-56028x05.1_14174_c1",
-        "nmdc:wfmgas-13-56028x05.1_14597_c1",
-        "nmdc:wfmgas-13-56028x05.1_16115_c1",
-        "nmdc:wfmgas-13-56028x05.1_16261_c1",
-        "nmdc:wfmgas-13-56028x05.1_16795_c1",
-        "nmdc:wfmgas-13-56028x05.1_16943_c1",
-        "nmdc:wfmgas-13-56028x05.1_17208_c1",
-        "nmdc:wfmgas-13-56028x05.1_17245_c1",
-        "nmdc:wfmgas-13-56028x05.1_17383_c1",
-        "nmdc:wfmgas-13-56028x05.1_17783_c1",
-        "nmdc:wfmgas-13-56028x05.1_18468_c1",
-        "nmdc:wfmgas-13-56028x05.1_18553_c1",
-        "nmdc:wfmgas-13-56028x05.1_18858_c1",
-        "nmdc:wfmgas-13-56028x05.1_19302_c1",
-        "nmdc:wfmgas-13-56028x05.1_19824_c1",
-        "nmdc:wfmgas-13-56028x05.1_20316_c1",
-        "nmdc:wfmgas-13-56028x05.1_20787_c1",
-        "nmdc:wfmgas-13-56028x05.1_21029_c1",
-        "nmdc:wfmgas-13-56028x05.1_21435_c1",
-        "nmdc:wfmgas-13-56028x05.1_21475_c1",
-        "nmdc:wfmgas-13-56028x05.1_21484_c1",
-        "nmdc:wfmgas-13-56028x05.1_21518_c1",
-        "nmdc:wfmgas-13-56028x05.1_21685_c1",
-        "nmdc:wfmgas-13-56028x05.1_21809_c1",
-        "nmdc:wfmgas-13-56028x05.1_21924_c1",
-        "nmdc:wfmgas-13-56028x05.1_21958_c1",
-        "nmdc:wfmgas-13-56028x05.1_22186_c1",
-        "nmdc:wfmgas-13-56028x05.1_22271_c1",
-        "nmdc:wfmgas-13-56028x05.1_22516_c1",
-        "nmdc:wfmgas-13-56028x05.1_22514_c1",
-        "nmdc:wfmgas-13-56028x05.1_22777_c1",
-        "nmdc:wfmgas-13-56028x05.1_23003_c1",
-        "nmdc:wfmgas-13-56028x05.1_23115_c1",
-        "nmdc:wfmgas-13-56028x05.1_23204_c1",
-        "nmdc:wfmgas-13-56028x05.1_23239_c1",
-        "nmdc:wfmgas-13-56028x05.1_23352_c1",
-        "nmdc:wfmgas-13-56028x05.1_23445_c1",
-        "nmdc:wfmgas-13-56028x05.1_23505_c1",
-        "nmdc:wfmgas-13-56028x05.1_23571_c1",
-        "nmdc:wfmgas-13-56028x05.1_24047_c1",
-        "nmdc:wfmgas-13-56028x05.1_24749_c1",
-        "nmdc:wfmgas-13-56028x05.1_24981_c1",
-        "nmdc:wfmgas-13-56028x05.1_25059_c1",
-        "nmdc:wfmgas-13-56028x05.1_25526_c1",
-        "nmdc:wfmgas-13-56028x05.1_26162_c1",
-        "nmdc:wfmgas-13-56028x05.1_26376_c1",
-        "nmdc:wfmgas-13-56028x05.1_26773_c1",
-        "nmdc:wfmgas-13-56028x05.1_26816_c1",
-        "nmdc:wfmgas-13-56028x05.1_26891_c1",
-        "nmdc:wfmgas-13-56028x05.1_27179_c1",
-        "nmdc:wfmgas-13-56028x05.1_27272_c1",
-        "nmdc:wfmgas-13-56028x05.1_27358_c1",
-        "nmdc:wfmgas-13-56028x05.1_27411_c1",
-        "nmdc:wfmgas-13-56028x05.1_27550_c1",
-        "nmdc:wfmgas-13-56028x05.1_28892_c1",
-        "nmdc:wfmgas-13-56028x05.1_29003_c1",
-        "nmdc:wfmgas-13-56028x05.1_29238_c1",
-        "nmdc:wfmgas-13-56028x05.1_29324_c1",
-        "nmdc:wfmgas-13-56028x05.1_29771_c1",
-        "nmdc:wfmgas-13-56028x05.1_29878_c1",
-        "nmdc:wfmgas-13-56028x05.1_30248_c1",
-        "nmdc:wfmgas-13-56028x05.1_30476_c1",
-        "nmdc:wfmgas-13-56028x05.1_30587_c1",
-        "nmdc:wfmgas-13-56028x05.1_31160_c1",
-        "nmdc:wfmgas-13-56028x05.1_31834_c1",
-        "nmdc:wfmgas-13-56028x05.1_31922_c1",
-        "nmdc:wfmgas-13-56028x05.1_31971_c1",
-        "nmdc:wfmgas-13-56028x05.1_32244_c1",
-        "nmdc:wfmgas-13-56028x05.1_32605_c1",
-        "nmdc:wfmgas-13-56028x05.1_32623_c1",
-        "nmdc:wfmgas-13-56028x05.1_32832_c1",
-        "nmdc:wfmgas-13-56028x05.1_33068_c1",
-        "nmdc:wfmgas-13-56028x05.1_33334_c1",
-        "nmdc:wfmgas-13-56028x05.1_33438_c1",
-        "nmdc:wfmgas-13-56028x05.1_33855_c1",
-        "nmdc:wfmgas-13-56028x05.1_34035_c1",
-        "nmdc:wfmgas-13-56028x05.1_34120_c1",
-        "nmdc:wfmgas-13-56028x05.1_34140_c1",
-        "nmdc:wfmgas-13-56028x05.1_34133_c1",
-        "nmdc:wfmgas-13-56028x05.1_34177_c1",
-        "nmdc:wfmgas-13-56028x05.1_34481_c1",
-        "nmdc:wfmgas-13-56028x05.1_34728_c1",
-        "nmdc:wfmgas-13-56028x05.1_34843_c1",
-        "nmdc:wfmgas-13-56028x05.1_35665_c1",
-        "nmdc:wfmgas-13-56028x05.1_35772_c1",
-        "nmdc:wfmgas-13-56028x05.1_35995_c1"
-      ]
+      "members_id": ["nmdc:wfmgas-13-56028x05.1_7_c1", "nmdc:wfmgas-13-56028x05.1_7_c2"]
     }
   ],
   "too_short_contig_num": 2005162,
diff --git a/tests/test_db2.json b/tests/test_db2.json
new file mode 100644
index 00000000..b4a5225d
--- /dev/null
+++ b/tests/test_db2.json
@@ -0,0 +1,21 @@
+{
+      "id": "nmdc:wfmag-20-abcd1234.1",
+      "type": "nmdc:MagsAnalysis",
+      "name": "Metagenome Assembled Genomes Analysis for nmdc:wfmags-20-abcd1234.1",
+      "has_input": [
+        "nmdc:dobj-13-abcd1234",
+        "nmdc:dobj-14-abcd1234",
+        "nmdc:dobj-15-abcd1234",
+        "nmdc:dobj-19-abcd1234"
+      ],
+        "has_output": [
+            "nmdc:dobj-21-abcd1234"
+        ],
+      "execution_resource": "JGI",
+      "git_url": "https://github.com/microbiomedata/metaMAGs",
+      "started_at_time": "2024-10-18T15:36:17.490112+00:00",
+      "was_informed_by": "nmdc:omprc-11-importT",
+      "ended_at_time": "2024-10-18T15:36:17.490117+00:00",
+      "version": "v1.0.6"
+    }
+
diff --git a/tests/test_imports.py b/tests/test_imports.py
index ccc0eb8e..b3614777 100644
--- a/tests/test_imports.py
+++ b/tests/test_imports.py
@@ -1,8 +1,17 @@
 import os
 import shutil
 from nmdc_automation.import_automation.activity_mapper import GoldMapper
+from nmdc_automation.models.nmdc import DataObject
+from nmdc_schema.nmdc import Database
 from pytest import fixture
+import importlib.resources
+import yaml
+from functools import lru_cache
+import linkml.validator
+from linkml_runtime.dumpers import yaml_dumper
+from linkml_runtime.loaders import json_loader
 from time import time
+from unittest.mock import patch
 
 
 
@@ -11,61 +20,150 @@
 #TODO NEXT: add test for import-mt.yaml similar to what is in test_workflow_process.py
 
 @fixture
-def gold_mapper(mock_api, base_test_dir, test_data_dir):
+def gold_mapper(mock_nmdc_runtime_api, base_test_dir, gold_import_files, gold_import_dir):
     """
     Base test function for code related to importing JGI records.
     """
     yaml_file = base_test_dir / "import_test.yaml"
-    test_files = [test_data_dir / "test_pfam.gff",
-                  test_data_dir / "test_cog.gff",
-                  test_data_dir / "test_2.tar.gz",
-                  test_data_dir / "test_72.tar.gz"]
-    # proj_dir = os.path.abspath("./test_data")
-    site_conf = base_test_dir / "site_configuration_test.toml"
     nucleotide_sequencing_id = "nmdc:omprc-11-importT"
     root_dir = f"/tmp/{nucleotide_sequencing_id}"
     if os.path.exists(root_dir):
         shutil.rmtree(root_dir)
-    gm = GoldMapper("1", test_files, nucleotide_sequencing_id, yaml_file, test_data_dir, site_conf)
+    gm = GoldMapper("1", gold_import_files, nucleotide_sequencing_id, yaml_file, gold_import_dir, mock_nmdc_runtime_api)
     gm.root_dir = root_dir
     return gm
 
 
-def test_workflow_execution_mapper(gold_mapper):
+@lru_cache(maxsize=None)
+def get_nmdc_materialized():
+    with importlib.resources.open_text("nmdc_schema", "nmdc_materialized_patterns.yaml") as f:
+        return yaml.safe_load(f)
+
+
+def test_gold_mapper_map_sequencing_data(gold_mapper):
     """
-    Test the creation of workflow execution records and data objects that are has_output of those workflow execution subclasses.
+    Test that the gold mapper creates data objects for the sequencing data, and
+    provides an update to be applied to the has_output list of the sequencing data generation
     """
-    gold_mapper.unique_object_mapper()
-    gold_mapper.multiple_objects_mapper()
-    gold_mapper.workflow_execution_mapper()
-    gold_mapper.post_nmdc_database_object()
-    db = gold_mapper.get_database_object_dump()
-    #This should return 4 workflow_execution_set records becuase that is the number of records with Import:true in the config file
-    #note that if these records were tested against the actual schema they would fail b/c workflow executions can't have has_output be null.
-    assert len(db.workflow_execution_set) == 4
-    # gff files are 1:1 with data objects that are has_output of nmdc:MetagenomeAnnotation
-    # *tar.gz files should be combined into a single data object that is has_output of nmdc:MagsAnalysis
-    assert len(db.data_object_set) == 3
-
-
-def test_unique_object_mapper(gold_mapper):
+    exp_num_data_objects = 1    # There is only one sequencing data file from the gold import files fixture
+    exp_dobj_id = "nmdc:dobj-11-abcd1234"   # From the mock API minter response
+    exp_dobj_type = "Metagenome Raw Reads"  # From the gold_import_files fixture
+    exp_nucleotide_sequencing_id = "nmdc:omprc-11-importT"  # From the gold mapper fixture
+    exp_update = {
+        "collection": "data_generation_set",
+        "filter": {"id": exp_nucleotide_sequencing_id},
+        "update": {"$addToSet": {"has_output": [exp_dobj_id]}}
+    }
+    # Sequencing data does not get a URL
+    exp_url = None
+    exp_name = '52834.4.466476.GATCGAGT-GATCGAGT.fastq.gz'
+    exp_description = 'Metagenome Raw Reads for nmdc:omprc-11-importT'
+
+    db, update = gold_mapper.map_sequencing_data()
+    # Database assertions
+    assert db
+    assert isinstance(db, Database)
+    assert db.data_object_set
+    data_objects = db.data_object_set
+    assert len(data_objects) == exp_num_data_objects
+    # Data object assertions
+    dobj = data_objects[0]
+    assert isinstance(dobj, DataObject)
+    assert str(dobj.data_object_type) == exp_dobj_type
+    assert dobj.id == exp_dobj_id
+    assert dobj.name == exp_name
+    assert dobj.description == exp_description
+    assert dobj.url == exp_url
+    assert dobj.file_size_bytes
+    assert dobj.md5_checksum
+
+    # Update assertions
+    assert update
+    assert update == exp_update
+
+
+def test_gold_mapper_map_data_unique(gold_mapper):
     """
-    This test counts the number of files from gold_mapper where the data object creation should be 1:1.
+    Test that the gold mapper creates data objects for the data files other
+    than the sequencing data
     """
-    gold_mapper.unique_object_mapper()
-    assert len(gold_mapper.nmdc_db.data_object_set) == 2
-    assert len(gold_mapper.objects) == 2
+    initial_num_data_objects = 1
+    db, update = gold_mapper.map_sequencing_data()
+    # sanity check
+    assert len(db.data_object_set) == initial_num_data_objects
+        # two unique data files from the gold import files fixture get added to the database
+    exp_data_object_types = [
+        "Clusters of Orthologous Groups (COG) Annotation GFF",
+        "Pfam Annotation GFF",
+        "Metagenome Raw Reads",
+        "Annotation Amino Acid FASTA",
+        "Filtered Sequencing Reads",
+        "Assembly Contigs",
+    ]
+
+    exp_nucleotide_sequencing_id = "nmdc:omprc-11-importT"  # From the gold mapper fixture
+
+    db, do_map = gold_mapper.map_data(db)
+    assert db
+    assert len(db.data_object_set) == len(exp_data_object_types)
+    data_objects = db.data_object_set
+    for dobj in data_objects:
+        assert str(dobj.data_object_type) in exp_data_object_types
+        assert isinstance(dobj, DataObject)
+        # sequencing data object should not have a URL
+        if str(dobj.data_object_type) == "Metagenome Raw Reads":
+            assert not dobj.url
+        else:
+            assert dobj.url
+            assert exp_nucleotide_sequencing_id in dobj.url
+            assert exp_nucleotide_sequencing_id in dobj.description
 
 
-def test_multiple_object_mapper(gold_mapper):
+def test_gold_mapper_map_data_multiple(gold_mapper):
     """
-    This test counts the number of files from gold_mapper where the data object creation should be many:1.  JGI stores each binning file 
-    individually whereas NMDC combines all the records into a single tar.gz file.
+    Test that the mapper is able to combine multiple data files into a single data object.
     """
-    gold_mapper.multiple_objects_mapper()
-    # Add assertions to check if the method works as expected
-    assert len(gold_mapper.nmdc_db.data_object_set) == 1
-    print(gold_mapper.nmdc_db.data_object_set)
-    assert len(gold_mapper.objects) == 1
-    #check that the data object url gets made correctly for the multiple object mapper function.
-    assert "https://data.microbiomedata.org/data/nmdc:omprc-11-importT/nmdc:abcd.1/nmdc_abcd.1_hqmq_bin.zip" in (do["url"] for do in gold_mapper.nmdc_db.data_object_set) 
+    initial_num_data_objects = 1
+    db, update = gold_mapper.map_sequencing_data()
+    # sanity check
+    assert len(db.data_object_set) == initial_num_data_objects
+    exp_num_data_objects = 2    # two files are combined into a single data object
+
+    db, do_map = gold_mapper.map_data(db, unique=False)
+    assert db
+    assert len(db.data_object_set) == exp_num_data_objects
+
+
+def test_gold_mapper_map_workflow_executions(gold_mapper, ):
+    """
+    Test that the gold mapper creates workflow execution records and data objects that are has_output of those workflow execution subclasses.
+    """
+
+    # setup
+    db, update = gold_mapper.map_sequencing_data()
+    db, do_map = gold_mapper.map_data(db)
+    db, do_map = gold_mapper.map_data(db, unique=False)
+
+    # test
+    db = gold_mapper.map_workflow_executions(db)
+    assert db.workflow_execution_set
+
+
+    # test that the db is valid according to the schema
+    nmdc_materialized = get_nmdc_materialized()
+    # db is a schema object, so we need to convert it to a dictionary
+
+    db_dict = yaml.safe_load(yaml_dumper.dumps(db))
+
+    validation_report = linkml.validator.validate(db_dict, nmdc_materialized, "Database")
+
+    assert not validation_report.results, f"Validation error: {validation_report.results[0].message}"
+
+
+
+
+
+
+
+
+
diff --git a/tests/test_models.py b/tests/test_models.py
index 1d9aa4ec..8fb00898 100644
--- a/tests/test_models.py
+++ b/tests/test_models.py
@@ -1,20 +1,18 @@
 """ Test cases for the models module. """
 import json
-
+import pytest
 from bson import ObjectId
 from pathlib import Path
-from pytest import mark
-from nmdc_automation.workflow_automation.models import(
-    DataObject,
-    Job,
-    JobOutput,
-    JobWorkflow,
-    WorkflowProcessNode,
-    workflow_process_factory,
-)
+from pytest import mark, raises
+from nmdc_automation.models.nmdc import DataObject, workflow_process_factory
+from nmdc_automation.models.workflow import Job, JobOutput, JobWorkflow, WorkflowProcessNode
 from nmdc_automation.workflow_automation.workflows import load_workflow_configs
 from tests.fixtures import db_utils
 
+from linkml_runtime.dumpers import yaml_dumper
+import yaml
+
+
 def test_workflow_process_factory(fixtures_dir):
     """ Test the workflow_process_factory function. """
     record_types = {
@@ -33,6 +31,35 @@ def test_workflow_process_factory(fixtures_dir):
         wfe = workflow_process_factory(record)
         assert wfe.type == record_type
 
+
+def test_workflow_process_factory_incorrect_id(fixtures_dir):
+    record = json.load(open(fixtures_dir / "models/metagenome_annotation_record.json"))
+    # Change the id to an incorrect value - this would be an assembly id
+    record["id"] = "nmdc:wfmgas-11-009f3582.1"
+    with pytest.raises(ValueError) as excinfo:
+        workflow_process_factory(record, validate=True)
+    assert "'nmdc:wfmgas-11-009f3582.1' does not match" in str(excinfo.value)
+
+
+
+
+
+def test_workflow_process_factory_data_generation_invalid_analyte_category(fixtures_dir):
+    record = json.load(open(fixtures_dir / "models/nucleotide_sequencing_record.json"))
+    record["analyte_category"] = "Something Invalid"
+
+    with raises(ValueError) as excinfo:
+        wfe = workflow_process_factory(record)
+
+
+
+def test_workflow_process_factory_metagenome_assembly_with_invalid_execution_resource(fixtures_dir):
+    record = json.load(open(fixtures_dir / "models/metagenome_assembly_record.json"))
+    record["execution_resource"] = "Something Invalid"
+    with raises(ValueError) as excinfo:
+        wfe = workflow_process_factory(record)
+
+
 def test_workflow_process_factory_mags_with_mags_list(fixtures_dir):
     record = json.load(open(fixtures_dir / "models/mags_analysis_record.json"))
     mga = workflow_process_factory(record)
@@ -50,6 +77,7 @@ def test_process_factory_with_db_record():
     wfe = workflow_process_factory(record)
     assert wfe.type == "nmdc:NucleotideSequencing"
 
+
 @mark.parametrize("record_file, record_type", [
     ("mags_analysis_record.json", "nmdc:MagsAnalysis"),
     ("metagenome_annotation_record.json", "nmdc:MetagenomeAnnotation"),
@@ -90,16 +118,15 @@ def test_data_object_creation_from_records(fixtures_dir):
         assert data_obj.type == "nmdc:DataObject"
         assert data_obj.id == record["id"]
         assert data_obj.name == record["name"]
-        assert data_obj.data_object_type == record["data_object_type"]
+        assert str(data_obj.data_object_type) == record["data_object_type"]
 
-        data_obj_dict = data_obj.as_dict()
+        data_obj_dict = yaml.safe_load(yaml_dumper.dumps(data_obj))
         assert data_obj_dict == record
 
 
 def test_data_object_creation_from_db_records(test_db, fixtures_dir):
     db_utils.reset_db(test_db)
     db_utils.load_fixture(test_db, "data_object_set.json")
-    # db_utils.read_json("data_object_set.json")
 
     db_records = test_db["data_object_set"].find()
     db_records = list(db_records)
@@ -109,7 +136,7 @@ def test_data_object_creation_from_db_records(test_db, fixtures_dir):
         assert data_obj.type == "nmdc:DataObject"
         assert data_obj.id == db_record["id"]
         assert data_obj.name == db_record["name"]
-        assert data_obj.data_object_type == db_record["data_object_type"]
+        assert str(data_obj.data_object_type) == db_record["data_object_type"]
         assert data_obj.description == db_record["description"]
         assert data_obj.url == db_record["url"]
         assert data_obj.file_size_bytes == db_record.get("file_size_bytes")
@@ -122,6 +149,40 @@ def test_data_object_creation_from_db_records(test_db, fixtures_dir):
         assert data_obj_dict == db_record
 
 
+def test_data_object_creation_invalid_data_object_type():
+    record = {
+        "id": "nmdc:dobj-11-rawreads1",
+        "name": "metaG_R1_001.fastq.gz",
+        "description": "Sequencing results for metaG_R1",
+        "md5_checksum": "ed9467e690babb683b024ed47dd97b85",
+        "data_object_type": "Something Invalid",
+        "type": "nmdc:DataObject",
+        "url": "https://portal.nersc.gov"
+    }
+    with raises(ValueError) as excinfo:
+        data_obj = DataObject(**record)
+
+    # Test with a valid data object type
+    record.update({"data_object_type": "Metagenome Raw Reads"})
+    data_obj = DataObject(**record)
+    assert str(data_obj.data_object_type) == "Metagenome Raw Reads"
+
+
+def test_data_object_creation_invalid_data_category():
+    record = {
+        "id": "nmdc:dobj-11-qcstats",
+        "name": "nmdc_wfrqc-11-metag.1_filterStats.txt",
+        "description": "Reads QC summary for nmdc:wfrqc-11-metag1.1",
+        "file_size_bytes": 123456,
+        "md5_checksum": "7172cd332a734e002c88b35827acd991",
+        "data_object_type": "QC Statistics",
+        "data_category": "Something Invalid",
+        "url": "https://data.microbiomedata.org",
+        "type": "nmdc:DataObject"
+    }
+    with raises(ValueError) as excinfo:
+        data_obj = DataObject(**record)
+
 def test_job_output_creation():
     outputs = [
         {
diff --git a/tests/test_nmdcapi.py b/tests/test_nmdcapi.py
index 646e4c62..060c3200 100644
--- a/tests/test_nmdcapi.py
+++ b/tests/test_nmdcapi.py
@@ -3,7 +3,7 @@
 import os
 
 
-def test_basics(mock_api, requests_mock, site_config_file):
+def test_basics(requests_mock, site_config_file):
     n = nmdcapi(site_config_file)
 
     # Add decode description
@@ -14,7 +14,7 @@ def test_basics(mock_api, requests_mock, site_config_file):
     assert "metadata" in resp
 
 
-def test_objects(mock_api, requests_mock, site_config_file, test_data_dir):
+def test_objects(requests_mock, site_config_file, test_data_dir):
     n = nmdcapi(site_config_file)
 
     requests_mock.post("http://localhost/objects", json={})
@@ -37,7 +37,7 @@ def test_objects(mock_api, requests_mock, site_config_file, test_data_dir):
     assert "a" in resp
 
 
-def test_list_funcs(mock_api, requests_mock, site_config_file, test_data_dir):
+def test_list_funcs(requests_mock, site_config_file, test_data_dir):
     n = nmdcapi(site_config_file)
     mock_resp = json.load(open(test_data_dir / "mock_jobs.json"))
 
@@ -55,7 +55,7 @@ def test_list_funcs(mock_api, requests_mock, site_config_file, test_data_dir):
     assert resp is not None
 
 
-def test_update_op(mock_api, requests_mock, site_config_file):
+def test_update_op(requests_mock, site_config_file):
     n = nmdcapi(site_config_file)
 
     mock_resp = {'metadata': {"b": "c"}}
@@ -69,7 +69,7 @@ def test_update_op(mock_api, requests_mock, site_config_file):
     assert "b" in resp["metadata"]
 
 
-def test_jobs(mock_api, requests_mock, site_config_file):
+def test_jobs(requests_mock, site_config_file):
     n = nmdcapi(site_config_file)
 
     requests_mock.get("http://localhost/jobs/abc", json="jobs/")
diff --git a/tests/test_wfutils.py b/tests/test_wfutils.py
index fde4942c..6e05344f 100644
--- a/tests/test_wfutils.py
+++ b/tests/test_wfutils.py
@@ -4,7 +4,7 @@
     WorkflowStateManager,
     _json_tmp,
 )
-from nmdc_automation.workflow_automation.models import DataObject, workflow_process_factory
+from nmdc_automation.models.nmdc import DataObject, workflow_process_factory
 from nmdc_schema.nmdc import MagsAnalysis, EukEval
 import io
 import json
diff --git a/tests/test_workflow_process.py b/tests/test_workflow_process.py
index f8813353..1cf81058 100644
--- a/tests/test_workflow_process.py
+++ b/tests/test_workflow_process.py
@@ -105,7 +105,7 @@ def test_get_required_data_objects_by_id(test_db, workflows_config_dir, workflow
     # get a unique list of the data object types
     do_types = set()
     for do in required_data_object_map.values():
-        do_types.add(do.data_object_type)
+        do_types.add(do.data_object_type.code.text)
     # check that the expected data object types are present
     for do_type in exp_do_types:
         assert do_type in do_types