seer-pas-sdk 0.3.4__py3-none-any.whl → 1.1.0__py3-none-any.whl

seer_pas_sdk/core/sdk.py

@@ -1,17 +1,21 @@
 from tqdm import tqdm
 
 import deprecation
+import numpy as np
 import os
-import jwt
 import requests
 import urllib.request
 import ssl
 
+
 from typing import List as _List, Tuple as _Tuple
 
 from ..common import *
 from ..auth import Auth
 from ..objects.volcanoplot import VolcanoPlotBuilder
+from ..objects.headers import *
+
+import warnings
 
 
 class SeerSDK:
@@ -31,7 +35,7 @@ class SeerSDK:
         try:
             self._auth = Auth(username, password, instance)
 
-            self._auth.get_token()
+            self._auth._login()
             print(f"User '{username}' logged in.\n")
 
             if not tenant:
@@ -45,16 +49,43 @@ class SeerSDK:
                 print("Logging into home tenant...")
                 # If an error occurs while directing the user to a tenant, default to home tenant.
                 print(f"You are now active in {self.get_active_tenant_name()}")
+        except ServerError as e:
+            raise e
         except Exception as e:
             raise ValueError(
                 f"Could not log in.\nPlease check your credentials and/or instance: {e}."
             )
 
-    def _get_auth_headers(self, use_multi_tenant=True):
+    def logout(self):
+        """
+        Perform a logout operation for the current user of the SDK instance.
+
+        Returns
+        -------
+        success : bool
+            Boolean denoting whether the logout operation was successful.
+        """
+        if self._auth.has_valid_token():
+            self._auth._logout()
+            return True
+        else:
+            print("The user's session is expired. No action taken.")
+            return False
+
+    def __del__(self):
+        """
+        Destructor for the SeerSDK class. Logs out the user when the object is deleted.
+        """
+        if self._auth.has_valid_token():
+            self._auth._logout()
+
+    def _get_auth_headers(self, caller, use_multi_tenant=True):
         id_token, access_token = self._auth.get_token()
         header = {
             "Authorization": id_token,
             "Access-Token": access_token,
+            "x-seer-source": "sdk",
+            "x-seer-id": f"{self._auth.version}/{caller}",
         }
         if use_multi_tenant:
             multi_tenant = {
@@ -64,10 +95,10 @@ class SeerSDK:
             header.update(multi_tenant)
         return header
 
-    def _get_auth_session(self, use_multi_tenant=True):
+    def _get_auth_session(self, caller, use_multi_tenant=True):
         sess = requests.Session()
 
-        sess.headers.update(self._get_auth_headers(use_multi_tenant))
+        sess.headers.update(self._get_auth_headers(caller, use_multi_tenant))
 
         return sess
 
@@ -80,7 +111,7 @@ class SeerSDK:
         response : list[dict]
             A list of tenant objects pertaining to the user.
         """
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getusertenants") as s:
             response = s.get(f"{self._auth.url}api/v1/usertenants")
 
             if response.status_code != 200:
@@ -162,7 +193,7 @@ class SeerSDK:
                 "Invalid tenant identifier. Tenant was not switched."
             )
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("switchtenant") as s:
             response = s.put(
                 self._auth.url + "api/v1/users/tenant",
                 json={
@@ -242,7 +273,7 @@ class SeerSDK:
 
         URL = f"{self._auth.url}api/v1/usergroups"
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getspaces") as s:
             spaces = s.get(URL)
 
             if spaces.status_code != 200:
@@ -251,6 +282,11 @@ class SeerSDK:
                 )
             return spaces.json()
 
+    @deprecation.deprecated(
+        deprecated_in="1.1.0",
+        removed_in="2.0.0",
+        details="This method is deprecated and will be removed in a future release. Use `find_plates` instead.",
+    )
     def get_plates(
         self, plate_id: str = None, plate_name: str = None, as_df: bool = False
     ):
@@ -293,7 +329,7 @@ class SeerSDK:
             938  5b05d440-6610-11ea-96e3-d5a4dab4ebf6  ...       None
             939  9872e3f0-544e-11ea-ad9e-1991e0725494  ...       None
 
-        >>> seer_sdk.get_plate_metadata(id="YOUR_PLATE_ID_HERE")
+        >>> seer_sdk.get_plates(id="YOUR_PLATE_ID_HERE")
         >>> [{ "id": ... }]
         """
 
@@ -307,7 +343,7 @@ class SeerSDK:
         else:
             params = dict()
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getplates") as s:
 
             plates = s.get(
                 f"{URL}/{plate_id}" if plate_id else URL,
@@ -327,6 +363,172 @@ class SeerSDK:
 
         return res if not as_df else dict_to_df(res)
 
+    def get_plate(self, plate_id: str = None, plate_name: str = None):
+        """
+        Fetches a plate.
+
+        Parameters
+        ----------
+        plate_id : str, optional
+            ID of the plate to be fetched, defaulted to None.
+
+        plate_name : str, optional
+            Name of the plate to be fetched, defaulted to None.
+
+        Returns
+        -------
+        plate: dict
+            A plate object.
+        """
+        if not (bool(plate_id) ^ bool(plate_name)):
+            raise ValueError(
+                "You must provide either plate_id or plate_name, but not both."
+            )
+
+        if plate_id:
+            URL = f"{self._auth.url}api/v1/plates/{plate_id}"
+            with self._get_auth_session("getplate") as s:
+                plates = s.get(URL)
+                if plates.status_code != 200:
+                    raise ValueError(
+                        "Invalid request. Please check your parameters."
+                    )
+                res = plates.json()
+                spaces = {
+                    x["id"]: x["usergroup_name"] for x in self.get_spaces()
+                }
+                if "tenant_id" in res:
+                    del res["tenant_id"]
+                if "user_group" in res:
+                    res["space"] = spaces.get(res["user_group"], "General")
+                    del res["user_group"]
+                if "id" in res:
+                    res["plate_uuid"] = res["id"]
+                return res
+        else:
+            res = self.find_plates(plate_name=plate_name)
+            if not res:
+                raise ValueError(f"No plate found with name '{plate_name}'.")
+            elif len(res) > 1:
+                raise ValueError(
+                    f"Multiple plates found with name '{plate_name}'. Please specify a plate_id."
+                )
+            else:
+                return res[0]
+
+    def find_plates(
+        self,
+        plate_id: str = None,
+        plate_name: str = None,
+        project_id: str = None,
+        project_name: str = None,
+        as_df: bool = False,
+    ):
+        """
+        Fetches a list of plates for the authenticated user. If no `plate_id` is provided, returns all plates for the authenticated user. If `plate_id` is provided, returns the plate with the given `plate_id`, provided it exists.
+
+        Parameters
+        ----------
+        plate_id : str, optional
+            ID of the plate to be fetched, defaulted to None.
+        plate_name : str, optional
+            Name of the plate to be fetched, defaulted to None.
+        project_id: str, optional
+            ID of the project to filter plates by, defaulted to None.
+        project_name : str, optional
+            Name of the project to filter plates by, defaulted to None.
+        as_df: bool
+            whether the result should be converted to a DataFrame, defaulted to None.
+
+        Returns
+        -------
+        plates: list[dict] or DataFrame
+            List/DataFrame of plate objects for the authenticated user.
+
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> seer_sdk.find_plates()
+        >>> [
+                { "id": ... },
+                { "id": ... },
+                ...
+            ]
+        >>> seer_sdk.find_plates(as_df=True)
+        >>>                                        id  ... user_group
+            0    a7c12190-15da-11ee-bdf1-bbaa73585acf  ...       None
+            1    8c3b1480-15da-11ee-bdf1-bbaa73585acf  ...       None
+            2    6f158840-15da-11ee-bdf1-bbaa73585acf  ...       None
+            3    1a8a2920-15da-11ee-bdf1-bbaa73585acf  ...       None
+            4    7ab47f40-15d9-11ee-bdf1-bbaa73585acf  ...       None
+            ..                                    ...  ...        ...
+            935  8fa91c00-6621-11ea-96e3-d5a4dab4ebf6  ...       None
+            936  53180b20-6621-11ea-96e3-d5a4dab4ebf6  ...       None
+            937  5c31fe90-6618-11ea-96e3-d5a4dab4ebf6  ...       None
+            938  5b05d440-6610-11ea-96e3-d5a4dab4ebf6  ...       None
+            939  9872e3f0-544e-11ea-ad9e-1991e0725494  ...       None
+
+        >>> seer_sdk.find_plates(id="YOUR_PLATE_ID_HERE")
+        >>> [{ "id": ... }]
+        """
+
+        URL = f"{self._auth.url}api/v1/plates"
+        res = []
+
+        if project_id or project_name:
+            if project_name and not project_id:
+                samples = self.find_samples(
+                    project_name=project_name, as_df=False
+                )
+            else:
+                samples = self.find_samples(project_id=project_id, as_df=False)
+            plate_ids = {
+                x.get("plate_uuid") for x in samples if "plate_uuid" in x
+            }
+            res = [self.get_plate(plate_id=x) for x in plate_ids]
+            return res if not as_df else dict_to_df(res)
+
+        if not plate_id and not plate_name:
+            params = {"all": "true"}
+        elif plate_id:
+            params = {"searchFields": "id", "searchItem": plate_id}
+        elif plate_name:
+            params = {"searchFields": "plate_name", "searchItem": plate_name}
+        else:
+            params = dict()
+
+        spaces = {x["id"]: x["usergroup_name"] for x in self.get_spaces()}
+        with self._get_auth_session("findplates") as s:
+
+            plates = s.get(
+                URL,
+                params=params,
+            )
+            if plates.status_code != 200:
+                raise ValueError(
+                    "Invalid request. Please check your parameters."
+                )
+
+            res = plates.json()["data"]
+
+            for entry in res:
+                if "tenant_id" in entry:
+                    del entry["tenant_id"]
+                if "user_group" in entry:
+                    entry["space"] = spaces.get(entry["user_group"], "General")
+                    del entry["user_group"]
+                if "id" in entry:
+                    entry["plate_uuid"] = entry["id"]
+        if (not res) and as_df:
+            return pd.DataFrame(columns=PLATE_COLUMNS)
+        return res if not as_df else dict_to_df(res)
+
+    @deprecation.deprecated(
+        deprecated_in="1.1.0",
+        removed_in="2.0.0",
+        details="This method is deprecated and will be removed in a future release. Use `find_projects` instead.",
+    )
     def get_projects(
         self,
         project_id: str = None,
@@ -393,7 +595,7 @@ class SeerSDK:
         else:
             params = {"searchFields": "id", "searchItem": project_id}
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getprojects") as s:
 
             projects = s.get(URL, params=params)
             if projects.status_code != 200:
@@ -416,8 +618,172 @@ class SeerSDK:
                 entry["raw_file_path"] = entry["raw_file_path"][
                     location(entry["raw_file_path"]) :
                 ]
+
+        return res if not as_df else dict_to_df(res)
+
+    def get_project(self, project_id: str = None, project_name: str = None):
+        """
+        Fetches a project.
+
+        Parameters
+        ----------
+        project_id: str, optional
+            ID of the project to be fetched, defaulted to None.
+
+        project_name: str, optional
+            Name of the project to be fetched, defaulted to None.
+
+        Returns
+        -------
+        projects: dict
+            A project object.
+        """
+        if not (bool(project_id) ^ bool(project_name)):
+            raise ValueError(
+                "You must provide either project_id or project_name, but not both."
+            )
+
+        if project_id:
+            URL = f"{self._auth.url}api/v1/projects/{project_id}"
+            with self._get_auth_session("getproject") as s:
+                projects = s.get(URL)
+                if projects.status_code != 200:
+                    raise ValueError(
+                        "Invalid request. Please check your parameters."
+                    )
+                res = projects.json()
+                spaces = {
+                    x["id"]: x["usergroup_name"] for x in self.get_spaces()
+                }
+                if "tenant_id" in res:
+                    del res["tenant_id"]
+                if "user_group" in res:
+                    res["space"] = spaces.get(res["user_group"], "General")
+                    del res["user_group"]
+                plate_ids = {
+                    x["plate_uuid"]
+                    for x in self.find_samples(project_id=res["id"])
+                }
+                res["plate_uuids"] = list(plate_ids)
+                return res
+        else:
+            res = self.find_projects(project_name=project_name)
+            if not res:
+                raise ValueError(
+                    f"No project found with name '{project_name}'."
+                )
+            elif len(res) > 1:
+                raise ValueError(
+                    f"Multiple projects found with name '{project_name}'. Please specify a project_id."
+                )
+            else:
+                return res[0]
+
+    def find_projects(
+        self,
+        project_id: str = None,
+        project_name: str = None,
+        as_df: bool = False,
+    ):
+        """
+        Fetches a list of projects. If no `project_id` is provided, returns all projects. If `project_id` is provided, returns the project with the given `project_id`, provided it exists.
+
+        Parameters
+        ----------
+        project_id: str, optional
+            Project ID of the project to be fetched, defaulted to None.
+        as_df: bool
+            whether the result should be converted to a DataFrame, defaulted to False.
+
+        Returns
+        -------
+        projects: list[dict] or DataFrame
+            DataFrame or list of project objects.
+
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> seer_sdk.get_projects()
+        >>> [
+                { "project_name": ... },
+                { "project_name": ... },
+                ...
+            ]
+
+        >>> seer_sdk.get_projects(as_df=True)
+        >>>                                        id  ... user_group
+            0    a7c12190-15da-11ee-bdf1-bbaa73585acf  ...       None
+            1    8c3b1480-15da-11ee-bdf1-bbaa73585acf  ...       None
+            2    6f158840-15da-11ee-bdf1-bbaa73585acf  ...       None
+            3    1a8a2920-15da-11ee-bdf1-bbaa73585acf  ...       None
+            4    7ab47f40-15d9-11ee-bdf1-bbaa73585acf  ...       None
+            ..                                    ...  ...        ...
+            935  8fa91c00-6621-11ea-96e3-d5a4dab4ebf6  ...       None
+            936  53180b20-6621-11ea-96e3-d5a4dab4ebf6  ...       None
+            937  5c31fe90-6618-11ea-96e3-d5a4dab4ebf6  ...       None
+            938  5b05d440-6610-11ea-96e3-d5a4dab4ebf6  ...       None
+            939  9872e3f0-544e-11ea-ad9e-1991e0725494  ...       None
+
+        >>> seer_sdk.find_projects(project_id="YOUR_PROJECT_ID_HERE")
+        >>> [{ "project_name": ... }]
+        """
+
+        URL = f"{self._auth.url}api/v1/projects"
+        res = []
+        if not project_id and not project_name:
+            params = {"all": "true"}
+        elif project_name:
+            params = {
+                "searchFields": "project_name",
+                "searchItem": project_name,
+            }
+        else:
+            params = {"searchFields": "id", "searchItem": project_id}
+
+        with self._get_auth_session("findprojects") as s:
+
+            projects = s.get(URL, params=params)
+            if projects.status_code != 200:
+                raise ValueError(
+                    "Invalid request. Please check your parameters."
+                )
+            res = projects.json()["data"]
+
+        spaces = {x["id"]: x["usergroup_name"] for x in self.get_spaces()}
+        plate_name_to_plate_uuid = {
+            x["plate_name"]: x["plate_uuid"]
+            for x in self.find_plates(as_df=False)
+        }
+        for entry in res:
+            if "tenant_id" in entry:
+                del entry["tenant_id"]
+
+            if "raw_file_path" in entry:
+                # Simple lambda function to find the third occurrence of '/' in the raw file path
+                location = lambda s: len(s) - len(s.split("/", 3)[-1])
+                # Slicing the string from the location
+                entry["raw_file_path"] = entry["raw_file_path"][
+                    location(entry["raw_file_path"]) :
+                ]
+            if "user_group" in entry:
+                entry["space"] = spaces.get(entry["user_group"], "General")
+                del entry["user_group"]
+
+            if "plates" in entry:
+                entry["plate_uuids"] = [
+                    plate_name_to_plate_uuid[x] for x in entry["plates"]
+                ]
+
+        if not res and as_df:
+            return pd.DataFrame(columns=PROJECT_COLUMNS)
         return res if not as_df else dict_to_df(res)
 
+    @deprecation.deprecated(
+        deprecated_in="1.1.0",
+        removed_in="2.0.0",
+        details="This method is deprecated and will be removed in a future release. Use `find_samples` instead.",
+    )
     def get_samples(
         self,
         plate_id: str = None,
@@ -493,10 +859,10 @@ class SeerSDK:
         sample_params = {"all": "true"}
 
         if project_id or plate_id:
-            with self._get_auth_session() as s:
+            with self._get_auth_session("getsamples") as s:
                 if plate_id:
                     try:
-                        self.get_plates(plate_id)
+                        self.find_plates(plate_id=plate_id)
                     except:
                         raise ValueError("Plate ID is invalid.")
                     sample_params["plateId"] = plate_id
@@ -530,7 +896,7 @@ class SeerSDK:
                 )
             else:
                 res_df = self._get_analysis_samples(
-                    analysis_name=analysis_name, as_df=True, is_name=True
+                    analysis_name=analysis_name, as_df=True
                 )
 
         # apply post processing
@@ -549,26 +915,198 @@ class SeerSDK:
 
         return res_df.to_dict(orient="records") if not as_df else res_df
 
-    def _filter_samples_metadata(
+    def find_samples(
         self,
-        project_id: str,
-        filter: str,
-        sample_ids: list = None,
+        plate_id: str = None,
+        project_id: str = None,
+        project_name: str = None,
+        analysis_id: str = None,
+        analysis_name: str = None,
+        as_df: bool = False,
     ):
         """
-        ****************
-        [UNEXPOSED METHOD CALL]
-        ****************
-        Get samples given a filter and project_id.
+        Fetches a list of samples. If no parameters are provided, returns all samples. If `plate_id` or `project_id` is provided, returns samples associated with that plate or project. If `analysis_id` or `analysis_name` is provided, returns samples associated with that analysis.
 
         Parameters
         ----------
-        project_id : str
-            The project id.
-        filter : str
-            The filter to be applied. Acceptable values are 'control' or 'sample'.
-        sample_ids : list, optional
-            List of user provided sample ids
+        plate_id : str, optional
+            ID of the plate for which samples are to be fetched, defaulted to None.
+        plate_name : str, optional
+            Name of the plate to be fetched, defaulted to None.
+        project_id : str, optional
+            ID of the project for which samples are to be fetched, defaulted to None.
+        project_name : str, optional
+            Name of the project to filter plates by, defaulted to None.
+        analysis_id : str, optional
+            ID of the analysis for which samples are to be fetched, defaulted to None.
+        analysis_name : str, optional
+            Name of the analysis for which samples are to be fetched, defaulted to None.
+        as_df: bool
+            whether the result should be converted to a DataFrame, defaulted to False.
+
+        Returns
+        -------
+        samples: list[dict] or DataFrame
+            List/DataFrame of samples for the authenticated user.
+
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+
+        >>> seer_sdk.find_samples(plate_id="7ec8cad0-15e0-11ee-bdf1-bbaa73585acf")
+        >>> [
+                { "id": ... },
+                { "id": ... },
+                ...
+            ]
+
+        >>> seer_sdk.find_samples(as_df=True)
+        >>>                                     id  ...      control
+        0     812139c0-15e0-11ee-bdf1-bbaa73585acf  ...
+        1     803e05b0-15e0-11ee-bdf1-bbaa73585acf  ...  MPE Control
+        2     a9b26a40-15da-11ee-bdf1-bbaa73585acf  ...
+        3     a8fc87c0-15da-11ee-bdf1-bbaa73585acf  ...  MPE Control
+        4     8e322990-15da-11ee-bdf1-bbaa73585acf  ...
+        ...                                    ...  ...          ...
+        3624  907e1f40-6621-11ea-96e3-d5a4dab4ebf6  ...         C132
+        3625  53e59450-6621-11ea-96e3-d5a4dab4ebf6  ...         C132
+        3626  5d11b030-6618-11ea-96e3-d5a4dab4ebf6  ...         C132
+        3627  5bdf9270-6610-11ea-96e3-d5a4dab4ebf6  ...         C132
+        3628  dd607ef0-654c-11ea-8eb2-25a1cfd1163c  ...         C132
+        """
+
+        # Raise an error if none or more than one of the primary key parameters are passed in.
+        if (
+            sum(
+                [
+                    True if x else False
+                    for x in [plate_id, project_id, analysis_id, analysis_name]
+                ]
+            )
+            > 1
+        ):
+            raise ValueError(
+                "You must pass in no more than one of plate_id, project_id, analysis_id, analysis_name."
+            )
+
+        res = []
+        URL = f"{self._auth.url}api/v1/samples"
+
+        if project_name and not project_id:
+            projects = self.find_projects(project_name=project_name)
+            if not projects or len(projects) > 1:
+                raise ValueError(
+                    f"Project name '{project_name}' is invalid or ambiguous. Please specify a project_id."
+                )
+            project_id = projects[0]["id"]
+
+        sample_params = {"all": "true"}
+
+        if project_id or plate_id:
+            with self._get_auth_session("findsamples") as s:
+                if plate_id:
+                    search_name = "plate_id"
+                    search_value = plate_id
+                    sample_params["plateId"] = plate_id
+
+                else:
+                    search_name = "project_id"
+                    search_value = project_id
+                    sample_params["projectId"] = project_id
+
+            samples = s.get(URL, params=sample_params)
+            if samples.status_code != 200:
+                raise ValueError(
+                    f"Failed to fetch sample data for {search_name}: {search_value}."
+                )
+            res = samples.json()["data"]
+            if not res:
+                return (
+                    [] if not as_df else pd.DataFrame(columns=SAMPLE_COLUMNS)
+                )
+            res_df = dict_to_df(res)
+
+            # API returns empty strings if not a control, replace with None for filtering purposes
+            res_df["control"] = res_df["control"].apply(
+                lambda x: x if x else None
+            )
+        elif analysis_id or analysis_name:
+            if analysis_id:
+                res_df = self._get_analysis_samples(
+                    analysis_id=analysis_id, as_df=True
+                )
+            else:
+                res_df = self._get_analysis_samples(
+                    analysis_name=analysis_name, as_df=True
+                )
+        else:
+            with self._get_auth_session("findsamples") as s:
+                samples = s.get(URL, params=sample_params)
+                if samples.status_code != 200:
+                    raise ValueError(
+                        "Failed to fetch sample data for the authenticated user."
+                    )
+                res = samples.json()["data"]
+                res_df = dict_to_df(res)
+
+        if res_df.empty and as_df:
+            return pd.DataFrame(columns=SAMPLE_COLUMNS)
+
+        plate_uuid_to_id = {
+            x["plate_uuid"]: x["plate_id"] for x in self.find_plates()
+        }
+        # apply post processing
+        if "tenant_id" in res_df.columns:
+            res_df.drop(["tenant_id"], axis=1, inplace=True)
+
+        if "user_group" in res_df.columns:
+            spaces = {x["id"]: x["usergroup_name"] for x in self.get_spaces()}
+            res_df["space"] = res_df["user_group"].apply(
+                lambda x: spaces.get(x, "General")
+            )
+            res_df.drop(["user_group"], axis=1, inplace=True)
+        if "plate_id" in res_df.columns:
+            res_df["plate_uuid"] = res_df["plate_id"]
+            res_df["plate_id"] = res_df["plate_uuid"].apply(
+                lambda x: plate_uuid_to_id.get(x, None)
+            )
+
+        custom_columns = [
+            x["field_name"] for x in self._get_sample_custom_fields()
+        ]
+        res_df = res_df[
+            [
+                x
+                for x in res_df.columns
+                if not x.startswith("custom_") or x in custom_columns
+            ]
+        ]
+
+        if res_df.empty and as_df:
+            return pd.DataFrame(columns=SAMPLE_COLUMNS)
+        return res_df.to_dict(orient="records") if not as_df else res_df
+
+    def _filter_samples_metadata(
+        self,
+        project_id: str,
+        filter: str,
+        sample_ids: list = None,
+    ):
+        """
+        ****************
+        [UNEXPOSED METHOD CALL]
+        ****************
+        Get samples given a filter and project_id.
+
+        Parameters
+        ----------
+        project_id : str
+            The project id.
+        filter : str
+            The filter to be applied. Acceptable values are 'control' or 'sample'.
+        sample_ids : list, optional
+            List of user provided sample ids
 
         Returns
         -------
@@ -579,7 +1117,7 @@ class SeerSDK:
         -------
         >>> from core import SeerSDK
         >>> seer_sdk = SeerSDK()
-        >>> seer_sdk._get_samples_filter("FILTER", "PROJECT_ID")
+        >>> seer_sdk._filter_samples_metadata("FILTER", "PROJECT_ID")
         >>> {
                 "samples": [
                     {
@@ -600,7 +1138,7 @@ class SeerSDK:
                 "Invalid filter. Please choose between 'control' or 'sample'."
             )
 
-        df = self.get_samples(project_id=project_id, as_df=True)
+        df = self.find_samples(project_id=project_id, as_df=True)
 
         if filter == "control":
             df = df[~df["control"].isna()]
@@ -619,7 +1157,7 @@ class SeerSDK:
         """
         URL = f"{self._auth.url}api/v1/samplefields"
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getcustomcolumns") as s:
 
             fields = s.get(URL)
 
@@ -633,6 +1171,11 @@ class SeerSDK:
                 del entry["tenant_id"]
             return res
 
+    @deprecation.deprecated(
+        deprecated_in="1.1.0",
+        removed_in="2.0.0",
+        details="This method is deprecated and will be removed in a future release. Use `find_msruns` instead.",
+    )
     def get_msruns(self, sample_ids: list, as_df: bool = False):
         """
         Fetches MS data files for passed in `sample_ids` (provided they are valid and contain relevant files) for an authenticated user.
@@ -676,7 +1219,74 @@ class SeerSDK:
         res = []
         for sample_id in sample_ids:
 
-            with self._get_auth_session() as s:
+            with self._get_auth_session("getmsdatas") as s:
+
+                msdatas = s.post(URL, json={"sampleId": sample_id})
+
+                if msdatas.status_code != 200 or not msdatas.json()["data"]:
+                    raise ValueError(
+                        f"Failed to fetch MS data for sample ID={sample_id}."
+                    )
+
+                res += [x for x in msdatas.json()["data"]]
+
+        for entry in res:
+            if "tenant_id" in entry:
+                del entry["tenant_id"]
+
+            if "raw_file_path" in entry:
+                # Simple lambda function to find the third occurrence of '/' in the raw file path
+                location = lambda s: len(s) - len(s.split("/", 3)[-1])
+                # Slicing the string from the location
+                entry["raw_file_path"] = entry["raw_file_path"][
+                    location(entry["raw_file_path"]) :
+                ]
+        return res if not as_df else dict_to_df(res)
+
+    def find_msruns(self, sample_ids: list, as_df: bool = False):
+        """
+        Fetches MS data files for passed in `sample_ids` (provided they are valid and contain relevant files) for an authenticated user.
+
+        The function returns a dict containing DataFrame objects if the `df` flag is passed in as True, otherwise a nested dict object is returned instead.
+
+        Parameters
+        ----------
+        sample_ids : list
+            List of unique sample IDs.
+        as_df: bool
+            whether the result should be converted to a DataFrame, defaulted to False.
+
+        Returns
+        -------
+        res: list[dict] or DataFrame
+            List/DataFrame of plate objects for the authenticated user.
+
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> sample_ids = ["812139c0-15e0-11ee-bdf1-bbaa73585acf", "803e05b0-15e0-11ee-bdf1-bbaa73585acf"]
+
+        >>> seer_sdk.find_msruns(sample_ids)
+        >>> [
+            {"id": "SAMPLE_ID_1_HERE" ... },
+            {"id": "SAMPLE_ID_2_HERE" ... }
+        ]
+
+        >>> seer_sdk.find_msruns(sample_ids, as_df=True)
+        >>>                                      id  ... gradient
+            0  81c6a180-15e0-11ee-bdf1-bbaa73585acf  ...     None
+            1  816a9ed0-15e0-11ee-bdf1-bbaa73585acf  ...     None
+
+            [2 rows x 26 columns]
+        """
+
+        URL = f"{self._auth.url}api/v1/msdatas/items"
+
+        res = []
+        for sample_id in sample_ids:
+
+            with self._get_auth_session("findmsdatas") as s:
 
                 msdatas = s.post(URL, json={"sampleId": sample_id})
 
@@ -687,6 +1297,7 @@ class SeerSDK:
 
                 res += [x for x in msdatas.json()["data"]]
 
+        spaces = {x["id"]: x["usergroup_name"] for x in self.get_spaces()}
         for entry in res:
             if "tenant_id" in entry:
                 del entry["tenant_id"]
@@ -698,8 +1309,19 @@ class SeerSDK:
                 entry["raw_file_path"] = entry["raw_file_path"][
                     location(entry["raw_file_path"]) :
                 ]
+            if "user_group" in entry:
+                entry["space"] = spaces.get(entry["user_group"], "General")
+                del entry["user_group"]
+
+        if not res and as_df:
+            return pd.DataFrame(columns=MSRUN_COLUMNS)
         return res if not as_df else dict_to_df(res)
 
+    @deprecation.deprecated(
+        deprecated_in="1.1.0",
+        removed_in="2.0.0",
+        details="This method is deprecated and will be removed in a future release. Use `find_analysis_protocols` instead.",
+    )
     def get_analysis_protocols(
         self,
         analysis_protocol_name: str = None,
@@ -724,80 +1346,515 @@ class SeerSDK:
         protocols: list[dict]
             List of analysis protocol objects for the authenticated user.
 
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.get_analysis_protocols()
-        >>> [
-                { "id": ..., "analysis_protocol_name": ... },
-                { "id": ..., "analysis_protocol_name": ... },
-                ...
-            ]
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> seer_sdk.get_analysis_protocols()
+        >>> [
+                { "id": ..., "analysis_protocol_name": ... },
+                { "id": ..., "analysis_protocol_name": ... },
+                ...
+            ]
+
+        >>> seer_sdk.get_analysis_protocols(name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
+        >>> [{ "id": ..., "analysis_protocol_name": ... }]
+
+        >>> seer_sdk.get_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE")
+        >>> [{ "id": ..., "analysis_protocol_name": ... }]
+
+        >>> seer_sdk.get_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE", name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
+
+        >>> [{ "id": ..., "analysis_protocol_name": ... }] # in this case the id would supersede the inputted name.
+        """
+
+        URL = (
+            f"{self._auth.url}api/v1/analysisProtocols"
+            if not analysis_protocol_id
+            else f"{self._auth.url}api/v1/analysisProtocols/{analysis_protocol_id}"
+        )
+        res = []
+        params = {"all": "true"}
+
+        if analysis_protocol_name:
+            params.update(
+                {
+                    "searchFields": "analysis_protocol_name,offering_name",
+                    "searchItem": analysis_protocol_name,
+                }
+            )
+
+        with self._get_auth_session("getanalysisprotocols") as s:
+
+            protocols = s.get(URL, params=params)
+            if protocols.status_code != 200:
+                raise ValueError(
+                    "Invalid request. Please check your parameters."
+                )
+            if analysis_protocol_id:
+                res = [protocols.json()]
+            else:
+                res = protocols.json()["data"]
+
+            for entry in range(len(res)):
+                if "tenant_id" in res[entry]:
+                    del res[entry]["tenant_id"]
+
+                if "can_edit" in res[entry]:
+                    del res[entry]["can_edit"]
+
+                if "can_delete" in res[entry]:
+                    del res[entry]["can_delete"]
+
+                if "scope" in res[entry]:
+                    del res[entry]["scope"]
+
+                if "parameter_file_path" in res[entry]:
+                    # Simple lambda function to find the third occurrence of '/' in the raw file path
+                    location = lambda s: len(s) - len(s.split("/", 3)[-1])
+                    # Slicing the string from the location
+                    res[entry]["parameter_file_path"] = res[entry][
+                        "parameter_file_path"
+                    ][location(res[entry]["parameter_file_path"]) :]
+
+            return res if not as_df else dict_to_df(res)
+
+    def get_analysis_protocol(
+        self,
+        analysis_protocol_id: str = None,
+        analysis_protocol_name: str = None,
+    ):
+        """
+        Fetches an analysis protocol.
+
+        Args:
+            analysis_protocol_id (str, optional): id of the analysis protocol to be fetched. Defaults to None.
+            analysis_protocol_name (str, optional): name of the analysis protocol to be fetched. Defaults to None.
+        Returns:
+            dict: Analysis protocol object
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> seer_sdk.get_analysis_protocol(analysis_protocol_id="YOUR_ANALYSIS_PROTOCOL_ID_HERE")
+        >>> { "id": ..., "analysis_protocol_name": ... }
+        >>> seer_sdk.get_analysis_protocol(analysis_protocol_name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
+        >>> { "id": ..., "analysis_protocol_name": ... }
+        """
+
+        if not (bool(analysis_protocol_id) ^ bool(analysis_protocol_name)):
+            raise ValueError(
+                "You must provide either analysis_protocol_id or analysis_protocol_name, but not both."
+            )
+
+        if analysis_protocol_id:
+            URL = f"{self._auth.url}api/v1/analysisProtocols/{analysis_protocol_id}"
+            with self._get_auth_session("getanalysisprotocol") as s:
+                protocols = s.get(URL)
+                if protocols.status_code != 200:
+                    raise ValueError(
+                        "Invalid request. Please check your parameters."
+                    )
+                res = protocols.json()
+                spaces = {
+                    x["id"]: x["usergroup_name"] for x in self.get_spaces()
+                }
+                if "tenant_id" in res:
+                    del res["tenant_id"]
+                if "user_group" in res:
+                    res["space"] = spaces.get(res["user_group"], "General")
+                    del res["user_group"]
+                try:
+                    res["fasta"] = ",".join(
+                        self._get_analysis_protocol_fasta_filenames(
+                            analysis_protocol_id=res["id"],
+                            analysis_protocol_engine=res["analysis_engine"],
+                        )
+                    )
+                except:
+                    res["fasta"] = ""
+                return res
+        else:
+            res = self.find_analysis_protocols(
+                analysis_protocol_name=analysis_protocol_name
+            )
+            if not res:
+                raise ValueError(
+                    f"No analysis protocol found with name '{analysis_protocol_name}'."
+                )
+            elif len(res) > 1:
+                raise ValueError(
+                    f"Multiple analysis protocols found with name '{analysis_protocol_name}'. Please specify an analysis_protocol_id."
+                )
+            else:
+                return res[0]
+
+    def find_analysis_protocols(
+        self,
+        analysis_protocol_name: str = None,
+        analysis_protocol_id: str = None,
+        as_df: bool = False,
+    ):
+        """
+        Fetches a list of analysis protocols for the authenticated user. If no `analysis_protocol_id` is provided, returns all analysis protocols for the authenticated user. If `analysis_protocol_name` (and no `analysis_protocol_id`) is provided, returns the analysis protocol with the given name, provided it exists.
+
+        Parameters
+        ----------
+        analysis_protocol_id : str, optional
+            ID of the analysis protocol to be fetched, defaulted to None.
+
+        analysis_protocol_name : str, optional
+            Name of the analysis protocol to be fetched, defaulted to None.
+
+        as_df : bool, optional
+            whether the result should be converted to a DataFrame, defaulted to False.
+        Returns
+        -------
+        protocols: list[dict]
+            List of analysis protocol objects for the authenticated user.
+
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> seer_sdk.find_analysis_protocols()
+        >>> [
+                { "id": ..., "analysis_protocol_name": ... },
+                { "id": ..., "analysis_protocol_name": ... },
+                ...
+            ]
+
+        >>> seer_sdk.find_analysis_protocols(name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
+        >>> [{ "id": ..., "analysis_protocol_name": ... }]
+
+        >>> seer_sdk.find_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE")
+        >>> [{ "id": ..., "analysis_protocol_name": ... }]
+
+        >>> seer_sdk.find_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE", name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
+
+        >>> [{ "id": ..., "analysis_protocol_name": ... }] # in this case the id would supersede the inputted name.
+        """
+
+        URL = f"{self._auth.url}api/v1/analysisProtocols"
+        res = []
+        params = {"all": "true"}
+
+        if analysis_protocol_name:
+            params.update(
+                {
+                    "searchFields": "analysis_protocol_name,offering_name",
+                    "searchItem": analysis_protocol_name,
+                }
+            )
+        elif analysis_protocol_id:
+            params.update(
+                {"searchFields": "id", "searchItem": analysis_protocol_id}
+            )
+
+        with self._get_auth_session("findanalysisprotocols") as s:
+
+            protocols = s.get(URL, params=params)
+            if protocols.status_code != 200:
+                raise ValueError(
+                    "Invalid request. Please check your parameters."
+                )
+            res = protocols.json()["data"]
+
+            spaces = {x["id"]: x["usergroup_name"] for x in self.get_spaces()}
+            for entry in range(len(res)):
+                if "tenant_id" in res[entry]:
+                    del res[entry]["tenant_id"]
+
+                if "can_edit" in res[entry]:
+                    del res[entry]["can_edit"]
+
+                if "can_delete" in res[entry]:
+                    del res[entry]["can_delete"]
+
+                if "scope" in res[entry]:
+                    del res[entry]["scope"]
+
+                if "parameter_file_path" in res[entry]:
+                    # Simple lambda function to find the third occurrence of '/' in the raw file path
+                    location = lambda s: len(s) - len(s.split("/", 3)[-1])
+                    # Slicing the string from the location
+                    res[entry]["parameter_file_path"] = res[entry][
+                        "parameter_file_path"
+                    ][location(res[entry]["parameter_file_path"]) :]
+                if "user_group" in res[entry]:
+                    res[entry]["space"] = spaces.get(
+                        res[entry]["user_group"], "General"
+                    )
+                    del res[entry]["user_group"]
+
+                try:
+                    res[entry]["fasta"] = ",".join(
+                        self._get_analysis_protocol_fasta_filenames(
+                            analysis_protocol_id=res[entry]["id"],
+                            analysis_protocol_engine=res[entry].get(
+                                "analysis_engine", None
+                            ),
+                        )
+                    )
+                except:
+                    res[entry]["fasta"] = ""
+
+            if not res and as_df:
+                return pd.DataFrame(columns=ANALYSIS_PROTOCOL_COLUMNS)
+            return res if not as_df else dict_to_df(res)
+
+    @deprecation.deprecated(
+        deprecated_in="1.1.0",
+        removed_in="2.0.0",
+        details="This method is deprecated and will be removed in a future release. Use `find_analyses` instead.",
+    )
+    def get_analyses(
+        self,
+        analysis_id: str = None,
+        folder_id: str = None,
+        show_folders: bool = True,
+        analysis_only: bool = True,
+        project_id: str = None,
+        plate_name: str = None,
+        as_df=False,
+        **kwargs,
+    ):
+        """
+        Returns a list of analyses objects for the authenticated user. If no id is provided, returns all analyses for the authenticated user.
+        Search parameters may be passed in as keyword arguments to filter the results. Acceptable values are 'analysis_name', 'folder_name', 'description', 'notes', or 'number_msdatafile'.
+        Only search on a single field is supported.
+
+        Parameters
+        ----------
+        analysis_id : str, optional
+            ID of the analysis to be fetched, defaulted to None.
+
+        folder_id : str, optional
+            ID of the folder to be fetched, defaulted to None.
+
+        show_folders : bool, optional
+            Mark True if folder contents are to be returned in the response, i.e. recursive search, defaulted to True.
+            Will be disabled if an analysis id is provided.
+
+        analysis_only : bool, optional
+            Mark True if only analyses objects are to be returned in the response, defaulted to True.
+            If marked false, folder objects will also be included in the response.
+
+        project_id : str, optional
+            ID of the project to be fetched, defaulted to None.
+
+        plate_name : str, optional
+            Name of the plate to be fetched, defaulted to None.
+
+        as_df : bool, optional
+            whether the result should be converted to a DataFrame, defaulted to False.
+
+        **kwargs : dict, optional
+            Search keyword parameters to be passed in. Acceptable values are 'analysis_name', 'folder_name', 'analysis_protocol_name', 'description', 'notes', or 'number_msdatafile'.
+
+        Returns
+        -------
+        analyses: list[dict]
+            Contains a list of analyses objects for the authenticated user.
+
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> seer_sdk.get_analyses()
+        >>> [
+                {id: "YOUR_ANALYSIS_ID_HERE", ...},
+                {id: "YOUR_ANALYSIS_ID_HERE", ...},
+                {id: "YOUR_ANALYSIS_ID_HERE", ...}
+            ]
+
+        >>> seer_sdk.get_analyses("YOUR_ANALYSIS_ID_HERE")
+        >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
+
+        >>> seer_sdk.get_analyses(folder_name="YOUR_FOLDER_NAME_HERE")
+        >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
+
+        >>> seer_sdk.get_analyses(analysis_name="YOUR_ANALYSIS")
+        >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
+
+        >>> seer_sdk.get_analyses(description="YOUR_DESCRIPTION")
+        >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
+        """
+
+        URL = f"{self._auth.url}api/v1/analyses"
+        res = []
+
+        search_field = None
+        search_item = None
+        if kwargs:
+            if len(kwargs.keys()) > 1:
+                raise ValueError("Please include only one search parameter.")
+            search_field = list(kwargs.keys())[0]
+            search_item = kwargs[search_field]
+
+            if not search_item:
+                raise ValueError(
+                    f"Please provide a non null value for {search_field}"
+                )
+
+        if search_field and search_field not in [
+            "analysis_name",
+            "folder_name",
+            "analysis_protocol_name",
+            "description",
+            "notes",
+            "number_msdatafile",
+        ]:
+            raise ValueError(
+                "Invalid search field. Please choose between 'analysis_name', 'folder_name', 'analysis_protocol_name', 'description', 'notes', or 'number_msdatafile'."
+            )
+
+        with self._get_auth_session("getanalyses") as s:
 
-        >>> seer_sdk.get_analysis_protocols(name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
-        >>> [{ "id": ..., "analysis_protocol_name": ... }]
+            params = {"all": "true"}
+            if folder_id:
+                params["folder"] = folder_id
 
-        >>> seer_sdk.get_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE")
-        >>> [{ "id": ..., "analysis_protocol_name": ... }]
+            if search_field:
+                params["searchFields"] = search_field
+                params["searchItem"] = search_item
+                del params["all"]
 
-        >>> seer_sdk.get_analysis_protocols(id="YOUR_ANALYSIS_PROTOCOL_ID_HERE", name="YOUR_ANALYSIS_PROTOCOL_NAME_HERE")
+                if search_field == "folder_name":
+                    params["searchFields"] = "analysis_name"
 
-        >>> [{ "id": ..., "analysis_protocol_name": ... }] # in this case the id would supersede the inputted name.
-        """
+            if project_id:
+                params["projectId"] = project_id
 
-        URL = (
-            f"{self._auth.url}api/v1/analysisProtocols"
-            if not analysis_protocol_id
-            else f"{self._auth.url}api/v1/analysisProtocols/{analysis_protocol_id}"
-        )
-        res = []
-        params = {"all": "true"}
+            if plate_name:
+                params["plateName"] = plate_name
 
-        if analysis_protocol_name:
-            params.update(
-                {
-                    "searchFields": "analysis_protocol_name,offering_name",
-                    "searchItem": analysis_protocol_name,
-                }
+            analyses = s.get(
+                f"{URL}/{analysis_id}" if analysis_id else URL, params=params
             )
 
-        with self._get_auth_session() as s:
-
-            protocols = s.get(URL, params=params)
-            if protocols.status_code != 200:
+            if analyses.status_code != 200:
                 raise ValueError(
                     "Invalid request. Please check your parameters."
                 )
-            if analysis_protocol_id:
-                res = [protocols.json()]
+            if not analysis_id:
+                res = analyses.json()["data"]
+
             else:
-                res = protocols.json()["data"]
+                res = [analyses.json()["analysis"]]
 
+            folders = []
             for entry in range(len(res)):
                 if "tenant_id" in res[entry]:
                     del res[entry]["tenant_id"]
 
-                if "can_edit" in res[entry]:
-                    del res[entry]["can_edit"]
-
-                if "can_delete" in res[entry]:
-                    del res[entry]["can_delete"]
-
-                if "scope" in res[entry]:
-                    del res[entry]["scope"]
-
                 if "parameter_file_path" in res[entry]:
                     # Simple lambda function to find the third occurrence of '/' in the raw file path
                     location = lambda s: len(s) - len(s.split("/", 3)[-1])
+
                     # Slicing the string from the location
                     res[entry]["parameter_file_path"] = res[entry][
                         "parameter_file_path"
                     ][location(res[entry]["parameter_file_path"]) :]
 
+                if (
+                    show_folders
+                    and not analysis_id
+                    and res[entry]["is_folder"]
+                ):
+                    folders.append(res[entry]["id"])
+
+            # recursive solution to get analyses in folders
+            for folder in folders:
+                res += self.get_analyses(folder_id=folder)
+
+            if analysis_only:
+                res = [
+                    analysis for analysis in res if not analysis["is_folder"]
+                ]
             return res if not as_df else dict_to_df(res)
 
-    def get_analyses(
+    def get_analysis(
+        self,
+        analysis_id: str = None,
+        analysis_name: str = None,
+    ):
+        """Fetches an analysis.
+
+        Args:
+            analysis_id (str, optional): id of the analysis to be fetched. Defaults to None.
+            analysis_name (str, optional): name of the analysis to be fetched. Defaults to None.
+
+        Returns:
+            analysis : dict
+                Analysis object
+        Examples
+        -------
+        >>> from seer_pas_sdk import SeerSDK
+        >>> seer_sdk = SeerSDK()
+        >>> seer_sdk.get_analysis(analysis_id="YOUR_ANALYSIS_ID_HERE")
+        >>> { "id": ..., "analysis_name": ... }
+
+        """
+        if not (bool(analysis_id) ^ bool(analysis_name)):
+            raise ValueError(
+                "You must provide either analysis_id or analysis_name, but not both."
+            )
+
+        if analysis_id:
+            URL = f"{self._auth.url}api/v1/analyses/{analysis_id}"
+            with self._get_auth_session("getanalysis") as s:
+                analysis = s.get(URL)
+                if analysis.status_code != 200:
+                    raise ValueError(
+                        "Invalid request. Please check your parameters."
+                    )
+                res = analysis.json()["analysis"]
+                spaces = {
+                    x["id"]: x["usergroup_name"] for x in self.get_spaces()
+                }
+                if "tenant_id" in res:
+                    del res["tenant_id"]
+                if "user_group" in res:
+                    res["space"] = spaces.get(res["user_group"], "General")
+                    del res["user_group"]
+                if not res.get("is_folder") and res.get(
+                    "analysis_protocol_id"
+                ):
+                    analysis_protocol = self.get_analysis_protocol(
+                        analysis_protocol_id=res.get("analysis_protocol_id")
+                    )
+                    try:
+                        res["fasta"] = ",".join(
+                            self._get_analysis_protocol_fasta_filenames(
+                                analysis_protocol_id=res.get(
+                                    "analysis_protocol_id"
+                                ),
+                                analysis_protocol_engine=analysis_protocol.get(
+                                    "analysis_engine", None
+                                ),
+                            )
+                        )
+                    except Exception as e:
+                        print("Warning: Could not fetch fasta files.")
+                        res["fasta"] = None
+                else:
+                    res["fasta"] = None
+                return res
+        else:
+            res = self.find_analyses(analysis_name=analysis_name)
+            if not res:
+                raise ValueError(
+                    f"No analysis found with name '{analysis_name}'."
+                )
+            elif len(res) > 1:
+                raise ValueError(
+                    f"Multiple analyses found with name '{analysis_name}'. Please specify an analysis_id."
+                )
+            else:
+                return res[0]
+
+    def find_analyses(
         self,
         analysis_id: str = None,
         folder_id: str = None,
@@ -850,23 +1907,23 @@ class SeerSDK:
         -------
         >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.get_analyses()
+        >>> seer_sdk.find_analyses()
         >>> [
                 {id: "YOUR_ANALYSIS_ID_HERE", ...},
                 {id: "YOUR_ANALYSIS_ID_HERE", ...},
                 {id: "YOUR_ANALYSIS_ID_HERE", ...}
             ]
 
-        >>> seer_sdk.get_analyses("YOUR_ANALYSIS_ID_HERE")
+        >>> seer_sdk.find_analyses("YOUR_ANALYSIS_ID_HERE")
         >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
 
-        >>> seer_sdk.get_analyses(folder_name="YOUR_FOLDER_NAME_HERE")
+        >>> seer_sdk.find_analyses(folder_name="YOUR_FOLDER_NAME_HERE")
         >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
 
-        >>> seer_sdk.get_analyses(analysis_name="YOUR_ANALYSIS")
+        >>> seer_sdk.find_analyses(analysis_name="YOUR_ANALYSIS")
         >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
 
-        >>> seer_sdk.get_analyses(description="YOUR_DESCRIPTION")
+        >>> seer_sdk.find_analyses(description="YOUR_DESCRIPTION")
         >>> [{ id: "YOUR_ANALYSIS_ID_HERE", ...}]
         """
 
@@ -898,7 +1955,13 @@ class SeerSDK:
                 "Invalid search field. Please choose between 'analysis_name', 'folder_name', 'analysis_protocol_name', 'description', 'notes', or 'number_msdatafile'."
             )
 
-        with self._get_auth_session() as s:
+        if analysis_id:
+            try:
+                return [self.get_analysis(analysis_id=analysis_id)]
+            except:
+                return []
+
+        with self._get_auth_session("findanalyses") as s:
 
             params = {"all": "true"}
             if folder_id:
@@ -918,30 +1981,25 @@ class SeerSDK:
             if plate_name:
                 params["plateName"] = plate_name
 
-            analyses = s.get(
-                f"{URL}/{analysis_id}" if analysis_id else URL, params=params
-            )
+            analyses = s.get(URL, params=params)
 
             if analyses.status_code != 200:
                 raise ValueError(
                     "Invalid request. Please check your parameters."
                 )
-            if not analysis_id:
-                res = analyses.json()["data"]
-
-            else:
-                res = [analyses.json()["analysis"]]
+            res = analyses.json()["data"]
 
             folders = []
+            spaces = {x["id"]: x["usergroup_name"] for x in self.get_spaces()}
+            protocol_to_engine_map = dict()
             for entry in range(len(res)):
                 if "tenant_id" in res[entry]:
                     del res[entry]["tenant_id"]
 
                 if "parameter_file_path" in res[entry]:
-                    # Simple lambda function to find the third occurrence of '/' in the raw file path
+                    # Trim parameter file path to user visible attributes
                     location = lambda s: len(s) - len(s.split("/", 3)[-1])
 
-                    # Slicing the string from the location
                     res[entry]["parameter_file_path"] = res[entry][
                         "parameter_file_path"
                     ][location(res[entry]["parameter_file_path"]) :]
@@ -953,17 +2011,65 @@ class SeerSDK:
                 ):
                     folders.append(res[entry]["id"])
 
+                if "user_group" in res[entry]:
+                    res[entry]["space"] = spaces.get(
+                        res[entry]["user_group"], "General"
+                    )
+                    del res[entry]["user_group"]
+
+                if (not res[entry].get("is_folder")) and res[entry].get(
+                    "analysis_protocol_id"
+                ):
+                    if (
+                        res[entry]["analysis_protocol_id"]
+                        in protocol_to_engine_map
+                    ):
+                        analysis_protocol_engine = protocol_to_engine_map[
+                            res[entry]["analysis_protocol_id"]
+                        ]
+                    else:
+                        try:
+                            analysis_protocol = self.get_analysis_protocol(
+                                analysis_protocol_id=res[entry].get(
+                                    "analysis_protocol_id"
+                                )
+                            )
+                            analysis_protocol_engine = analysis_protocol.get(
+                                "analysis_engine", None
+                            )
+                            protocol_to_engine_map[
+                                res[entry]["analysis_protocol_id"]
+                            ] = analysis_protocol_engine
+                        except:
+                            analysis_protocol_engine = None
+                    try:
+                        res[entry]["fasta"] = ",".join(
+                            self._get_analysis_protocol_fasta_filenames(
+                                res[entry]["analysis_protocol_id"],
+                                analysis_protocol_engine=analysis_protocol_engine,
+                            )
+                        )
+                    except:
+                        print(
+                            f"Warning: Could not fetch fasta files for analysis {res[entry].get('analysis_name')}."
+                        )
+                        res[entry]["fasta"] = None
+                else:
+                    res[entry]["fasta"] = None
+
             # recursive solution to get analyses in folders
             for folder in folders:
-                res += self.get_analyses(folder_id=folder)
+                res += self.find_analyses(folder_id=folder)
 
             if analysis_only:
                 res = [
                     analysis for analysis in res if not analysis["is_folder"]
                 ]
+            if not res and as_df:
+                return pd.DataFrame(columns=ANALYSIS_COLUMNS)
             return res if not as_df else dict_to_df(res)
 
-    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="1.0.0")
+    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="2.0.0")
     def get_analysis_result_protein_data(
         self, analysis_id: str, link: bool = False, pg: str = None
     ):
@@ -981,7 +2087,7 @@ class SeerSDK:
             Protein group ID to filter dataframe results. Defaults to None.
 
         """
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysisresultprotein") as s:
             URL = f"{self._auth.url}api/v1/data"
             response = s.get(
                 f"{URL}/protein?analysisId={analysis_id}&retry=false"
@@ -1013,16 +2119,18 @@ class SeerSDK:
             else:
                 if not pg:
                     return {
-                        "protein_np": url_to_df(protein_data["npLink"]["url"]),
-                        "protein_panel": url_to_df(
+                        "protein_np": download_df(
+                            protein_data["npLink"]["url"]
+                        ),
+                        "protein_panel": download_df(
                             protein_data["panelLink"]["url"]
                         ),
                     }
                 else:
-                    protein_np = url_to_df(
+                    protein_np = download_df(
                         protein_data["npLink"]["url"]
                     ).query(f"`Protein Group` == '{pg}'")
-                    protein_panel = url_to_df(
+                    protein_panel = download_df(
                         protein_data["panelLink"]["url"]
                     ).query(f"`Protein Group` == '{pg}'")
 
@@ -1036,7 +2144,7 @@ class SeerSDK:
                         "protein_panel": protein_panel,
                     }
 
-    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="1.0.0")
+    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="2.0.0")
     def get_analysis_result_peptide_data(
         self, analysis_id: str, link: bool = False, peptide: str = None
     ):
@@ -1057,7 +2165,7 @@ class SeerSDK:
 
         """
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysisresultpeptide") as s:
             URL = f"{self._auth.url}api/v1/data"
             response = s.get(
                 f"{URL}/peptide?analysisId={analysis_id}&retry=false"
@@ -1089,16 +2197,18 @@ class SeerSDK:
             else:
                 if not peptide:
                     return {
-                        "peptide_np": url_to_df(peptide_data["npLink"]["url"]),
-                        "peptide_panel": url_to_df(
+                        "peptide_np": download_df(
+                            peptide_data["npLink"]["url"]
+                        ),
+                        "peptide_panel": download_df(
                             peptide_data["panelLink"]["url"]
                         ),
                     }
                 else:
-                    peptide_np = url_to_df(
+                    peptide_np = download_df(
                         peptide_data["npLink"]["url"]
                     ).query(f"Peptide == '{peptide}'")
-                    peptide_panel = url_to_df(
+                    peptide_panel = download_df(
                         peptide_data["panelLink"]["url"]
                     ).query(f"Peptide == '{peptide}'")
 
@@ -1121,7 +2231,7 @@ class SeerSDK:
         analysis_id : str
             ID of the analysis for which the data is to be fetched.
         """
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getsearchresultprotein") as s:
             URL = f"{self._auth.url}api/v1/data"
             response = s.get(
                 f"{URL}/protein?analysisId={analysis_id}&retry=false"
@@ -1167,7 +2277,7 @@ class SeerSDK:
 
         """
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getsearchresultpeptide") as s:
             URL = f"{self._auth.url}api/v1/data"
             response = s.get(
                 f"{URL}/peptide?analysisId={analysis_id}&retry=false"
@@ -1220,7 +2330,7 @@ class SeerSDK:
             List of files associated with the analysis.
         """
         try:
-            analysis_metadata = self.get_analyses(analysis_id)[0]
+            analysis_metadata = self.find_analyses(analysis_id)[0]
         except (IndexError, ServerError):
             raise ValueError("Invalid analysis ID.")
         except:
@@ -1233,7 +2343,7 @@ class SeerSDK:
         if folder:
             params["folderKey"] = folder
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("listsearchresultfiles") as s:
             response = s.get(
                 f"{self._auth.url}api/v2/analysisResultFiles/{analysis_id}",
                 params=params,
@@ -1284,47 +2394,54 @@ class SeerSDK:
 
         if analyte_type not in ["protein", "peptide", "precursor"]:
             raise ValueError(
-                "Invalid data type. Please choose between 'protein', 'peptide', or 'precursor'."
+                "Unknown analyte_type = '{analyte_type}'. Supported types are 'protein', 'peptide', or 'precursor'."
             )
 
         if rollup not in ["np", "panel"]:
             raise ValueError(
-                "Invalid file. Please choose between 'np', 'panel'."
+                "Unknown rollup = '{rollup}'. Supported rollup types are 'np' and 'panel'."
             )
 
         if analyte_type == "precursor" and rollup == "panel":
             raise ValueError(
-                "Precursor data is not available for panel rollup, please select np rollup."
+                "Precursor data is not available for panel rollup, use rollup = 'np' to get precursor data."
             )
 
+        # cast Sample Name to str to ensure correct interpretation of sample names like '001'
+        dtype = {"Sample Name": str}
+
         if analyte_type == "protein":
             if rollup == "np":
-                return url_to_df(
+                return download_df(
                     self._get_search_result_protein_data(analysis_id)[
                         "npLink"
-                    ]["url"]
+                    ]["url"],
+                    dtype=dtype,
                 )
             elif rollup == "panel":
-                return url_to_df(
+                return download_df(
                     self._get_search_result_protein_data(analysis_id)[
                         "panelLink"
-                    ]["url"]
+                    ]["url"],
+                    dtype=dtype,
                 )
         elif analyte_type == "peptide":
             if rollup == "np":
-                return url_to_df(
+                return download_df(
                     self._get_search_result_peptide_data(analysis_id)[
                         "npLink"
-                    ]["url"]
+                    ]["url"],
+                    dtype=dtype,
                 )
             elif rollup == "panel":
-                return url_to_df(
+                return download_df(
                     self._get_search_result_peptide_data(analysis_id)[
                         "panelLink"
-                    ]["url"]
+                    ]["url"],
+                    dtype=dtype,
                 )
         else:
-            return url_to_df(
+            return download_df(
                 self.get_search_result_file_url(
                     analysis_id, filename="report.tsv"
                 )["url"]
@@ -1344,18 +2461,21 @@ class SeerSDK:
         filename : str
             Name of the file to be fetched. Files can be case insensitive and without file extensions.
 
-        download_path : str
+        download_path : str, optional
             String flag denoting where the user wants the files downloaded. Can be local or absolute as long as the path is valid.
 
         Returns
         -------
-        None
-            Downloads the file to the specified path.
+        str
+            Path to the downloaded file.
         """
 
         if not download_path:
             download_path = os.getcwd()
 
+        if download_path.endswith("/"):
+            download_path = download_path.rstrip("/")
+
         if not analysis_id:
             raise ValueError("Analysis ID cannot be empty.")
 
@@ -1363,7 +2483,6 @@ class SeerSDK:
             raise ValueError(
                 "Please specify a valid folder path as download path."
             )
-
         file = self.get_search_result_file_url(analysis_id, filename)
         file_url = file["url"]
         filename = file["filename"]
@@ -1389,15 +2508,10 @@ class SeerSDK:
                     )
                     break
             except:
-                filename = filename.split("/")
-                name += "/" + "/".join(
-                    [filename[i] for i in range(len(filename) - 1)]
-                )
-                filename = filename[-1]
-                if not os.path.isdir(f"{name}/{filename}"):
-                    os.makedirs(f"{name}/")
-        print(f"File {filename} downloaded successfully to {download_path}.")
-        return
+                dirname = f"{download_path}/{os.path.dirname(filename)}"
+                if not os.path.isdir(f"{dirname}"):
+                    os.makedirs(f"{dirname}")
+        return f"{download_path}/{filename}"
 
     def get_search_result_file_url(self, analysis_id: str, filename: str):
         """
@@ -1416,12 +2530,19 @@ class SeerSDK:
         file_url: dict[str, str]
             Dictionary containing the 'url' and 'filename' of the file.
         """
+        pas_dirname = os.path.dirname(filename)
         if "." in filename:
             filename = ".".join(filename.split(".")[:-1])
         filename = filename.casefold()
 
+        if pas_dirname:
+            analysis_result_files = self.list_search_result_files(
+                analysis_id, folder=pas_dirname
+            )
+        else:
+            analysis_result_files = self.list_search_result_files(analysis_id)
+
         # Allow user to pass in filenames without an extension.
-        analysis_result_files = self.list_search_result_files(analysis_id)
         analysis_result_files_prefix_mapper = {
             (".".join(x.split(".")[:-1])).casefold(): x
             for x in analysis_result_files
@@ -1433,10 +2554,10 @@ class SeerSDK:
                 f"Filename {filename} not among the available analysis result files. Please use SeerSDK.list_search_result_files('{analysis_id}') to see available files for this analysis."
             )
 
-        analysis_metadata = self.get_analyses(analysis_id)[0]
+        analysis_metadata = self.get_analysis(analysis_id)
         if analysis_metadata.get("status") in ["Failed", None]:
             raise ValueError("Cannot generate links for failed searches.")
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getsearchresultfileurl") as s:
             file_url = s.post(
                 f"{self._auth.url}api/v1/analysisResultFiles/getUrl",
                 json={
@@ -1452,7 +2573,7 @@ class SeerSDK:
         response["filename"] = filename
         return response
 
-    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="1.0.0")
+    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="2.0.0")
     def get_analysis_result_files(
         self,
         analysis_id: str,
@@ -1578,7 +2699,7 @@ class SeerSDK:
                     continue
 
         links = {
-            k: url_to_df(v, is_tsv=k.endswith(".tsv"))
+            k: download_df(v, is_tsv=k.endswith(".tsv"))
             for k, v in links.items()
         }
         if download_path:
@@ -1595,7 +2716,7 @@ class SeerSDK:
 
         return links
 
-    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="1.0.0")
+    @deprecation.deprecated(deprecated_in="0.3.0", removed_in="2.0.0")
     def get_analysis_result(
         self,
         analysis_id: str,
@@ -1660,17 +2781,17 @@ class SeerSDK:
             analysis_id, link=True
         )
         links = {
-            "peptide_np": url_to_df(peptide_data["npLink"]["url"]),
-            "peptide_panel": url_to_df(peptide_data["panelLink"]["url"]),
-            "protein_np": url_to_df(protein_data["npLink"]["url"]),
-            "protein_panel": url_to_df(protein_data["panelLink"]["url"]),
+            "peptide_np": download_df(peptide_data["npLink"]["url"]),
+            "peptide_panel": download_df(peptide_data["panelLink"]["url"]),
+            "protein_np": download_df(protein_data["npLink"]["url"]),
+            "protein_panel": download_df(protein_data["panelLink"]["url"]),
         }
 
         if diann_report:
             diann_report_url = self._get_search_result_file_url(
                 analysis_id, "report.tsv"
             )
-            links["diann_report"] = url_to_df(diann_report_url["url"])
+            links["diann_report"] = download_df(diann_report_url["url"])
 
         if download_path:
             name = f"{download_path}/downloads/{analysis_id}"
@@ -1723,7 +2844,7 @@ class SeerSDK:
             raise ValueError("Analysis id cannot be empty.")
 
         try:
-            res = self.get_analyses(analysis_id)
+            res = self.find_analyses(analysis_id)
         except ValueError:
             return ValueError("Analysis not found. Your ID could be incorrect")
 
@@ -1757,12 +2878,12 @@ class SeerSDK:
             )
 
         if not analysis_id and analysis_name:
-            analysis_id = self.get_analyses(analysis_name=analysis_name)[0][
+            analysis_id = self.find_analyses(analysis_name=analysis_name)[0][
                 "id"
             ]
 
         URL = self._auth.url + "api/v2/groupanalysis/protein"
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getproteinresults") as s:
             res = s.post(
                 URL, json={"analysisId": analysis_id, "grouping": grouping}
             )
@@ -1826,12 +2947,12 @@ class SeerSDK:
             )
 
         if not analysis_id and analysis_name:
-            analysis_id = self.get_analyses(analysis_name=analysis_name)[0][
+            analysis_id = self.find_analyses(analysis_name=analysis_name)[0][
                 "id"
             ]
 
         URL = self._auth.url + "api/v2/groupanalysis/peptide"
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getpeptideresults") as s:
             res = s.post(
                 URL, json={"analysisId": analysis_id, "grouping": grouping}
             )
@@ -1901,7 +3022,7 @@ class SeerSDK:
             if not space
             else f"{self._auth.url}api/v1/msdataindex/filesinfolder?folder={folder}&userGroupId={space}"
         )
-        with self._get_auth_session() as s:
+        with self._get_auth_session("listmsdatafiles") as s:
 
             files = s.get(URL)
 
@@ -1912,7 +3033,7 @@ class SeerSDK:
             return files.json()["filesList"]
 
     def download_ms_data_files(
-        self, paths: _List[str], download_path: str, space: str = None
+        self, paths: _List[str], download_path: str = "", space: str = None
     ):
         """
         Downloads all MS data files for paths passed in the params to the specified download path.
@@ -1921,15 +3042,14 @@ class SeerSDK:
         ----------
         paths : list[str]
             List of paths to download.
-        download_path : str
-            Path to download the files to.
+        download_path : str, optional
+            Path to download the files to. Defaults to current working directory.
         space : str, optional
             ID of the user group to which the files belongs, defaulted to None.
 
         Returns
         -------
-        message: dict[str, str]
-            Contains the 'message' whether the files were downloaded or not.
+        list[str] : the list of paths to the downloaded files.
         """
 
         urls = []
@@ -1957,8 +3077,7 @@ class SeerSDK:
         tenant_id = self._auth.active_tenant_id
 
         for path in paths:
-            with self._get_auth_session() as s:
-
+            with self._get_auth_session("getmsdataindexurl") as s:
                 download_url = s.post(
                     URL,
                     json={
@@ -1972,6 +3091,8 @@ class SeerSDK:
                         "Could not download file. Please check if the backend is running."
                     )
                 urls.append(download_url.text)
+
+        downloads = []
         for i in range(len(urls)):
             filename = paths[i].split("/")[-1]
             url = urls[i]
@@ -1996,6 +3117,7 @@ class SeerSDK:
                             reporthook=download_hook(t),
                             data=None,
                         )
+                        downloads.append(f"{name}/{filename}")
                         break
                 except:
                     filename = filename.split("/")
@@ -2013,7 +3135,7 @@ class SeerSDK:
 
             print(f"Finished downloading {filename}\n")
 
-        return {"message": f"Files downloaded successfully to '{name}'"}
+        return downloads
 
     def get_group_analysis(
         self, analysis_id, group_analysis_id=None, **kwargs
@@ -2062,7 +3184,7 @@ class SeerSDK:
             URL = f"{URL}/{group_analysis_id}"
             params["id"] = group_analysis_id
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getgroupanalyses") as s:
             response = s.get(URL, params=params)
             if response.status_code != 200:
                 raise ServerError(
@@ -2141,7 +3263,7 @@ class SeerSDK:
         }
 
         # Pre-GA data call
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysisresultprotein") as s:
 
             protein_pre_data = s.post(
                 url=f"{URL}api/v2/groupanalysis/protein",
@@ -2156,7 +3278,7 @@ class SeerSDK:
 
             res["pre"]["protein"] = protein_pre_data
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysisresultpeptide") as s:
 
             peptide_pre_data = s.post(
                 url=f"{URL}api/v2/groupanalysis/peptide",
@@ -2172,7 +3294,7 @@ class SeerSDK:
             res["pre"]["peptide"] = peptide_pre_data
 
         # Post-GA data call
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getgroupanalysispost") as s:
             if group_analysis_id:
                 get_saved_result = self.get_group_analysis(
                     analysis_id=analysis_id,
@@ -2255,7 +3377,7 @@ class SeerSDK:
                                         'proteinId', 'intensity', 'sampleName', 'sampleId', 'condition','gene'
         """
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getgroupanalysisraw") as s:
 
             # API call 1 - get volcano plot data for filtered results and gene mapping
             builder = self.get_volcano_plot_data(
@@ -2411,7 +3533,7 @@ class SeerSDK:
 
         URL = f"{self._auth.url}api/v1/analysisqcpca"
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysispca") as s:
             json = {
                 "analysisIds": ",".join(analysis_ids),
                 "type": type,
@@ -2561,7 +3683,7 @@ class SeerSDK:
 
         URL = f"{self._auth.url}api/v1/analysishcluster"
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysishclust") as s:
             json = {
                 "analysisIds": ",".join(analysis_ids),
             }
@@ -2617,7 +3739,7 @@ class SeerSDK:
 
         URL = f"{self._auth.url}api/v1/groupanalysis/stringdb"
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getppinetwork") as s:
             json = {
                 "significantPGs": ",".join(significant_pgs),
             }
@@ -2698,7 +3820,7 @@ class SeerSDK:
             significantPGs=",".join(significant_pgs),
         )
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysisclusterheatmap") as s:
             URL = f"{self._auth.url}api/v2/clusterheatmap"
             response = s.post(URL, json=payload)
             if response.status_code != 200:
@@ -2737,7 +3859,7 @@ class SeerSDK:
         if not significant_pgs:
             raise ValueError("Significant pgs cannot be empty.")
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysisenrichmentplot") as s:
             json = {
                 "analysisId": analysis_id,
                 "significantPGs": significant_pgs,
@@ -2827,12 +3949,12 @@ class SeerSDK:
         if analysis_id:
             rows = [{"id": analysis_id}]
         else:
-            rows = self.get_analyses(analysis_name=analysis_name)
+            rows = self.find_analyses(analysis_name=analysis_name)
 
         resp = []
         for row in rows:
             URL = f"{self._auth.url}api/v1/analyses/samples/{row['id']}"
-            with self._get_auth_session() as s:
+            with self._get_auth_session("getanalysissamples") as s:
                 samples = s.get(URL)
                 try:
                     samples.raise_for_status()
@@ -2841,15 +3963,15 @@ class SeerSDK:
                 except:
                     continue
 
-        if not resp:
-            raise ServerError(
-                f"Could not retrieve samples for analysis {analysis_id or analysis_name}."
-            )
-
         resp = pd.DataFrame(resp)
         resp.drop_duplicates(subset=["id"], inplace=True)
         return resp if as_df else resp.to_dict(orient="records")
 
+    @deprecation.deprecated(
+        deprecated_in="1.1.0",
+        removed_in="2.0.0",
+        details="get_analysis_protocol_fasta is deprecated. Use download_analysis_protocol_fasta instead.",
+    )
     def get_analysis_protocol_fasta(self, analysis_id, download_path=None):
         if not analysis_id:
             raise ValueError("Analysis ID cannot be empty.")
@@ -2858,14 +3980,14 @@ class SeerSDK:
             download_path = os.getcwd()
 
         try:
-            analysis_protocol_id = self.get_analyses(analysis_id)[0][
+            analysis_protocol_id = self.find_analyses(analysis_id)[0][
                 "analysis_protocol_id"
             ]
         except (IndexError, KeyError):
             raise ValueError(f"Could not parse server response.")
 
         try:
-            analysis_protocol_engine = self.get_analysis_protocols(
+            analysis_protocol_engine = self.find_analysis_protocols(
                 analysis_protocol_id=analysis_protocol_id
             )[0]["analysis_engine"]
         except (IndexError, KeyError):
@@ -2887,7 +4009,7 @@ class SeerSDK:
                 f"Analysis protocol engine {analysis_protocol_engine} not supported for fasta download."
             )
 
-        with self._get_auth_session() as s:
+        with self._get_auth_session("getanalysisprotocolparameters") as s:
             response = s.get(URL)
             if response.status_code != 200:
                 raise ServerError("Request failed.")
@@ -2904,7 +4026,7 @@ class SeerSDK:
 
         URL = f"{self._auth.url}api/v1/analysisProtocolFiles/getUrl"
         for file in fasta_filenames:
-            with self._get_auth_session() as s:
+            with self._get_auth_session("getanalysisprotocolfilesurl") as s:
                 response = s.post(URL, json={"filepath": file})
                 if response.status_code != 200:
                     raise ServerError("Request failed.")
@@ -2935,3 +4057,172 @@ class SeerSDK:
                             os.makedirs(f"{download_path}")
 
                 print(f"Downloaded file to {download_path}/{file}")
+
+    def _get_analysis_protocol_fasta_filenames(
+        self, analysis_protocol_id: str, analysis_protocol_engine: str
+    ):
+        """
+        Helper function - Get the fasta file name(s) associated with a given analysis protocol and engine.
+            Args:
+                analysis_protocol_id (str): ID of the analysis protocol.
+                analysis_protocol_engine (str): Analysis engine of the analysis protocol.
+            Returns:
+                list[str]: A list of fasta file names associated with the analysis protocol.
+        """
+        analysis_protocol_engine = analysis_protocol_engine.lower()
+        if analysis_protocol_engine == "diann":
+            URL = f"{self._auth.url}api/v1/analysisProtocols/editableParameters/diann/{analysis_protocol_id}"
+        elif analysis_protocol_engine == "encyclopedia":
+            URL = f"{self._auth.url}api/v1/analysisProtocols/editableParameters/dia/{analysis_protocol_id}"
+        elif analysis_protocol_engine == "msfragger":
+            URL = f"{self._auth.url}api/v1/analysisProtocols/editableParameters/msfragger/{analysis_protocol_id}"
+        elif analysis_protocol_engine == "proteogenomics":
+            URL = f"{self._auth.url}api/v1/analysisProtocols/editableParameters/proteogenomics/{analysis_protocol_id}"
+        elif analysis_protocol_engine == "maxquant":
+            URL = f"{self._auth.url}api/v1/analysisProtocols/editableParameters/{analysis_protocol_id}"
+        else:
+            raise ValueError(
+                f"Analysis protocol engine {analysis_protocol_engine} not supported for fasta download."
+            )
+
+        with self._get_auth_session("getanalysisprotocolparameters") as s:
+            response = s.get(URL)
+            if response.status_code != 200:
+                raise ServerError("Failed to retrieve analysis protocol data.")
+            response = response.json()
+            if isinstance(response, dict):
+                response = response["editableParameters"]
+            fasta_filenames = (
+                np.array(
+                    [
+                        x["Value"]
+                        for x in response
+                        if x["Key"]
+                        in ["fasta", "fastaFilePath", "referencegenome"]
+                    ]
+                )
+                .flatten()
+                .tolist()
+            )
+            if not fasta_filenames:
+                raise ServerError("No fasta file name returned from server.")
+            return fasta_filenames
+
+    def get_analysis_protocol_fasta_link(
+        self, analysis_protocol_id=None, analysis_id=None, analysis_name=None
+    ):
+        """Get the download link(s) for the fasta file(s) associated with a given analysis protocol.
+        Args:
+            analysis_protocol_id (str,optional): ID of the analysis protocol. Defaults to None.
+            analysis_id (str, optional): ID of the analysis. Defaults to None.
+            analysis_name (str, optional): Name of the analysis. Defaults to None.
+
+        Returns:
+            list[dict]: A list of dictionaries containing the 'filename' and the 'url' to download the fasta file.
+        """
+        if analysis_name and (not analysis_id):
+            analyses = self.find_analyses(analysis_name=analysis_name)
+            if len(analyses) > 1:
+                raise ValueError(
+                    f"Multiple analyses found with name {analysis_name}. Please provide an analysis ID instead."
+                )
+            elif len(analyses) == 0:
+                raise ValueError(
+                    f"No analyses found with name {analysis_name}."
+                )
+            else:
+                analysis_id = analyses[0]["id"]
+
+        if not (bool(analysis_protocol_id) ^ bool(analysis_id)):
+            raise ValueError(
+                "Please provide either an analysis ID or an analysis protocol ID."
+            )
+
+        if not analysis_protocol_id:
+            try:
+                analysis_protocol_id = self.get_analysis(
+                    analysis_id=analysis_id
+                )["analysis_protocol_id"]
+            except KeyError:
+                raise ValueError(f"Could not parse server response.")
+
+        engine = self.get_analysis_protocol(
+            analysis_protocol_id=analysis_protocol_id
+        ).get("analysis_engine", None)
+        fasta_filenames = self._get_analysis_protocol_fasta_filenames(
+            analysis_protocol_id=analysis_protocol_id,
+            analysis_protocol_engine=engine,
+        )
+        URL = f"{self._auth.url}api/v1/analysisProtocolFiles/getUrl"
+        links = []
+        for file in fasta_filenames:
+            with self._get_auth_session("getanalysisprotocolfilesurl") as s:
+                filename = os.path.basename(file)
+                response = s.post(URL, json={"filepath": file})
+                if response.status_code != 200:
+                    print(
+                        f"ERROR: Could not retrieve download link for {filename}."
+                    )
+                    continue
+                url = response.json()["url"]
+                links.append({"filename": filename, "url": url})
+        return links
+
+    def download_analysis_protocol_fasta(
+        self,
+        analysis_protocol_id=None,
+        analysis_id=None,
+        analysis_name=None,
+        download_path=None,
+    ):
+        """Download the fasta file(s) associated with a given analysis protocol.
+
+        Args:
+            analysis_protocol_id (str,optional): ID of the analysis protocol. Defaults to None.
+            analysis_id (str, optional): ID of the analysis. Defaults to None.
+            analysis_name (str, optional): Name of the analysis. Defaults to None.
+            download_path (str, optional): Path to download the fasta file to. Defaults to current working directory.
+
+        Returns:
+            list[str] : The path to the downloaded fasta file(s).
+        """
+
+        links = [
+            (x["filename"], x["url"])
+            for x in self.get_analysis_protocol_fasta_link(
+                analysis_protocol_id=analysis_protocol_id,
+                analysis_id=analysis_id,
+                analysis_name=analysis_name,
+            )
+        ]
+        if not download_path:
+            download_path = os.getcwd()
+
+        downloads = []
+        for filename, url in links:
+            print(f"Downloading {filename}")
+            for _ in range(2):
+                try:
+                    with tqdm(
+                        unit="B",
+                        unit_scale=True,
+                        unit_divisor=1024,
+                        miniters=1,
+                        desc=f"Progress",
+                    ) as t:
+                        ssl._create_default_https_context = (
+                            ssl._create_unverified_context
+                        )
+                        urllib.request.urlretrieve(
+                            url,
+                            f"{download_path}/{filename}",
+                            reporthook=download_hook(t),
+                            data=None,
+                        )
+                        break
+                except:
+                    if not os.path.isdir(f"{download_path}"):
+                        os.makedirs(f"{download_path}")
+
+            downloads.append(f"{download_path}/{filename}")
+        return downloads