seer-pas-sdk 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

seer_pas_sdk/core/__init__.py

@@ -1,1307 +1 @@
-from tqdm import tqdm
-
-import os
-import jwt
-import requests
-import urllib.request
-import ssl
-import shutil
-
-from typing import List as _List
-
-from ..common import *
-from ..auth import Auth
-from ..objects import PlateMap
-
-
-class SeerSDK:
-    """
-    Object exposing SDK methods. Requires a username and password; the optional `instance` param denotes the instance of PAS (defaults to "US").
-
-    Examples
-    -------
-    >>> from seer_pas_sdk import SeerSDK
-    >>> USERNAME = "test"
-    >>> PASSWORD = "test-password"
-    >>> INSTANCE = "EU"
-    >>> seer_sdk = SeerSDK(USERNAME, PASSWORD, INSTANCE)
-    """
-
-    def __init__(self, username, password, instance="US"):
-        try:
-            self._auth = Auth(username, password, instance)
-
-            self._auth.get_token()
-
-            print(f"User '{username}' logged in.\n")
-
-        except:
-            raise ValueError(
-                "Could not log in.\nPlease check your credentials and/or instance."
-            )
-
-    def get_spaces(self):
-        """
-        Fetches a list of spaces for the authenticated user.
-
-        Returns
-        -------
-        spaces: list
-            List of space objects for the authenticated user.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.get_spaces()
-        >>> [
-                { "usergroup_name": ... },
-                { "usergroup_name": ... },
-                ...
-            ]
-        """
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}api/v1/usergroups"
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            spaces = s.get(URL)
-
-            if spaces.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Please check your parameters."
-                )
-            return spaces.json()
-
-    def get_plate_metadata(self, plate_id: str = None, 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.
-        df: bool
-            Boolean denoting whether the user wants the response back in JSON or a DataFrame object
-
-        Returns
-        -------
-        plates: list or DataFrame
-            List/DataFrame of plate objects for the authenticated user.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.get_plate_metadata()
-        >>> [
-                { "id": ... },
-                { "id": ... },
-                ...
-            ]
-        >>> seer_sdk.get_plate_metadata(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.get_plate_metadata(id="YOUR_PLATE_ID_HERE")
-        >>> [{ "id": ... }]
-        """
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}api/v1/plates"
-        res = []
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            plates = s.get(
-                f"{URL}/{plate_id}" if plate_id else URL,
-                params={"all": "true"},
-            )
-            if plates.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Please check your parameters."
-                )
-            if not plate_id:
-                res = plates.json()["data"]
-            else:
-                res = [plates.json()]
-
-            for entry in res:
-                del entry["tenant_id"]
-
-        return res if not df else dict_to_df(res)
-
-    def get_project_metadata(self, project_id: str = None, df: bool = False):
-        """
-        Fetches a list of projects for the authenticated user. If no `project_id` is provided, returns all projects for the authenticated user. 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.
-        df: bool
-            Boolean denoting whether the user wants the response back in JSON or a DataFrame object.
-
-        Returns
-        -------
-        projects: list or DataFrame
-            DataFrame or list of project objects for the authenticated user.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.get_project_metadata()
-        >>> [
-                { "project_name": ... },
-                { "project_name": ... },
-                ...
-            ]
-
-        >>> seer_sdk.get_project_metadata(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.get_project_metadata(id="YOUR_PROJECT_ID_HERE")
-        >>> [{ "project_name": ... }]
-        """
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = (
-            f"{self._auth.url}api/v1/projects"
-            if not project_id
-            else f"{self._auth.url}api/v1/projects/{project_id}"
-        )
-        res = []
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            projects = s.get(URL, params={"all": "true"})
-            if projects.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Please check your parameters."
-                )
-            if not project_id:
-                res = projects.json()["data"]
-            else:
-                res = [projects.json()]
-
-        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 df else dict_to_df(res)
-
-    def _get_samples_metadata(
-        self, plate_id: str = None, project_id: str = None, df: bool = False
-    ):
-        """
-        ****************
-        [UNEXPOSED METHOD CALL]
-        ****************
-
-        Fetches a list of samples for the authenticated user, filtered by `plate_id`. Returns all samples for the plate with the given `plate_id`, provided it exists.
-
-        If both `plate_id` and `project_id` are passed in, only the `plate_id` is validated first.
-
-        Parameters
-        ----------
-        plate_id : str, optional
-            ID of the plate for which samples are to be fetched, defaulted to None.
-        project_id : str, optional
-            ID of the project for which samples are to be fetched, defaulted to None.
-        df: bool
-            Boolean denoting whether the user wants the response back in JSON or a DataFrame object
-
-        Returns
-        -------
-        samples: list or DataFrame
-            List/DataFrame of samples for the authenticated user.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-
-        >>> seer_sdk._get_samples_metadata(plate_id="7ec8cad0-15e0-11ee-bdf1-bbaa73585acf")
-        >>> [
-                { "id": ... },
-                { "id": ... },
-                ...
-            ]
-
-        >>> seer_sdk._get_samples_metadata(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
-        """
-
-        if not plate_id and not project_id:
-            raise ValueError("You must pass in plate ID or project ID.")
-
-        res = []
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}api/v1/samples"
-        sample_params = {"all": "true"}
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            if plate_id:
-                try:
-                    self.get_plate_metadata(plate_id)
-                except:
-                    raise ValueError(
-                        "Plate ID is invalid. Please check your parameters and see if the backend is running."
-                    )
-                sample_params["plateId"] = plate_id
-
-            elif project_id:
-                try:
-                    self.get_project_metadata(project_id)
-                except:
-                    raise ValueError(
-                        "Project ID is invalid. Please check your parameters and see if the backend is running."
-                    )
-
-                sample_params["projectId"] = project_id
-
-            samples = s.get(URL, params=sample_params)
-            if samples.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Please check if your plate ID has any samples associated with it."
-                )
-            res = samples.json()["data"]
-
-            for entry in res:
-                del entry["tenant_id"]
-
-        # Exclude custom fields that don't belong to the tenant
-        res_df = dict_to_df(res)
-        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
-            ]
-        ]
-
-        return res_df.to_dict(orient="records") if not df else res_df
-
-    def get_sample_custom_fields(self):
-        """
-        Fetches a list of custom fields defined for the authenticated user.
-        """
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}api/v1/samplefields"
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            fields = s.get(URL)
-
-            if fields.status_code != 200:
-                raise ValueError(
-                    "Failed to fetch custom columns. Please check your connection."
-                )
-
-            res = fields.json()
-            for entry in res:
-                del entry["tenant_id"]
-            return res
-
-    def get_msdata(self, sample_ids: list, 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.
-        df: bool
-            Boolean denoting whether the user wants the response back in JSON or a DataFrame object.
-
-        Returns
-        -------
-        res: list 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.get_msdata(sample_ids)
-        >>> [
-            {"id": "SAMPLE_ID_1_HERE" ... },
-            {"id": "SAMPLE_ID_2_HERE" ... }
-        ]
-
-        >>> seer_sdk.get_msdata(sample_ids, df=True)
-        >>>                                      id  ... gradient
-            0  81c6a180-15e0-11ee-bdf1-bbaa73585acf  ...     None
-            1  816a9ed0-15e0-11ee-bdf1-bbaa73585acf  ...     None
-
-            [2 rows x 26 columns]
-        """
-        res = []
-        for sample_id in sample_ids:
-            ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-            HEADERS = {
-                "Authorization": f"{ID_TOKEN}",
-                "access-token": f"{ACCESS_TOKEN}",
-            }
-            URL = f"{self._auth.url}api/v1/msdatas/items"
-
-            with requests.Session() as s:
-                s.headers.update(HEADERS)
-
-                msdatas = s.post(URL, json={"sampleId": sample_id})
-
-                if msdatas.status_code != 200 or not msdatas.json()["data"]:
-                    raise ValueError(
-                        "Failed to fetch MS data for your plate ID."
-                    )
-
-                res.append(msdatas.json()["data"][0])
-
-        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 df else dict_to_df(res)
-
-    def get_plate(self, plate_id: str, df: bool = False):
-        """
-        Fetches MS data files for a `plate_id` (provided that the `plate_id` is valid and has samples associated with it) 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
-        ----------
-        plate_id : str, optional
-            ID of the plate for which samples are to be fetched, defaulted to None.
-        df: bool
-            Boolean denoting whether the user wants the response back in JSON or a DataFrame object
-
-        Returns
-        -------
-        res: list or DataFrame
-            List/DataFrame of MS data file objects for the authenticated user.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> plate_id = "7ec8cad0-15e0-11ee-bdf1-bbaa73585acf"
-
-        >>> seer_sdk.get_plate(plate_id)
-        >>> [
-            {"id": "PLATE_ID_1_HERE" ... },
-            {"id": "PLATE_ID_2_HERE" ... }
-        ]
-
-        >>> seer_sdk.get_plate(plate_id, df=True)
-        >>>                 id  ...   volume
-            0  PLATE_ID_1_HERE  ...     None
-            1  PLATE_ID_2_HERE  ...     None
-
-            [2 rows x 26 columns]
-        """
-        plate_samples = self._get_samples_metadata(plate_id=plate_id)
-        sample_ids = [sample["id"] for sample in plate_samples]
-        return self.get_msdata(sample_ids, df)
-
-    def get_project(
-        self, project_id: str, msdata: bool = False, df: bool = False
-    ):
-        """
-        Fetches samples (and MS data files) for a `project_id` (provided that the `project_id` is valid and has samples associated with it) for an authenticated user.
-
-        The function returns a DataFrame object if the `df` flag is passed in as True, otherwise a nested dict object is returned instead. If the both the `df` and `msdata` flags are passed in as True, then a nested DataFrame object is returned instead.
-
-        Parameters
-        ----------
-        project_id : str
-            ID of the project for which samples are to be fetched.
-        msdata: bool, optional
-            Boolean flag denoting whether the user wants relevant MS data files associated with the samples.
-        df: bool, optional
-            Boolean denoting whether the user wants the response back in JSON or a DataFrame object.
-
-        Returns
-        -------
-        res: list or DataFrame
-            List/DataFrame of plate objects for the authenticated user.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> project_id = "7e48e150-8a47-11ed-b382-bf440acece26"
-
-        >>> seer_sdk.get_project(project_id=project_id, msdata=False, df=False)
-        >>> {
-            "project_samples": [
-                {
-                    "id": "SAMPLE_ID_1_HERE",
-                    "sample_type": "Plasma",
-                    ...
-                    ...
-                },
-                {
-                    "id": "SAMPLE_ID_2_HERE",
-                    "sample_type": "Plasma",
-                    ...
-                    ...
-                }
-            ]
-        }
-
-        >>> seer_sdk.get_project(project_id=project_id, msdata=True, df=False)
-        >>> [
-                {
-                    "id": "SAMPLE_ID_1_HERE",
-                    "sample_type": "Plasma",
-                    ...
-                    ...
-                    "ms_data_files": [
-                        {
-                            "id": MS_DATA_FILE_ID_1_HERE,
-                            "tenant_id": "TENANT_ID_HERE",
-                            ...
-                            ...
-                        },
-                        {
-                            "id": MS_DATA_FILE_ID_1_HERE,
-                            "tenant_id": "TENANT_ID_HERE",
-                            ...
-                            ...
-                        }
-                    ]
-                },
-                {
-                    "id": "SAMPLE_ID_2_HERE",
-                    "sample_type": "Plasma",
-                    ...
-                    ...
-                    "ms_data_files": [
-                        {
-                            "id": MS_DATA_FILE_ID_2_HERE,
-                            "tenant_id": "TENANT_ID_HERE",
-                            ...
-                            ...
-                        },
-                        {
-                            "id": MS_DATA_FILE_ID_2_HERE,
-                            "tenant_id": "TENANT_ID_HERE",
-                            ...
-                            ...
-                        }
-                    ]
-                }
-            ]
-
-        >>> seer_sdk.get_project(project_id=project_id, msdata=True, df=True)
-        >>> id  ...                                                                           ms_data_files
-            0  829509f0-8a47-11ed-b382-bf440acece26  ...                                       id  ... g...
-            1  828d41c0-8a47-11ed-b382-bf440acece26  ...                                       id  ... g...
-            2  8294e2e0-8a47-11ed-b382-bf440acece26  ...                                       id  ... g...
-            3  8285eec0-8a47-11ed-b382-bf440acece26  ...                                       id  ... g...
-
-            [4 rows x 60 columns]
-        """
-        if not project_id:
-            return ValueError("No project ID specified.")
-
-        sample_ids = []
-        project_samples = self._get_samples_metadata(
-            project_id=project_id, df=False
-        )
-
-        if msdata:
-            sample_ids = [
-                sample["id"] for sample in project_samples
-            ]  # will always contain unique values
-            ms_data_files = self.get_msdata(sample_ids=sample_ids, df=False)
-
-            for ms_data_file in ms_data_files:
-                for sample_index in range(len(project_samples)):
-                    if (
-                        project_samples[sample_index]["id"]
-                        == ms_data_file["sample_id"]
-                    ):
-                        if "ms_data_file" not in project_samples[sample_index]:
-                            project_samples[sample_index]["ms_data_files"] = [
-                                ms_data_file
-                            ]
-                        else:
-                            project_samples[sample_index][
-                                "ms_data_files"
-                            ].append(ms_data_file)
-
-        if df:
-            for sample_index in range(len(project_samples)):
-                if "ms_data_files" in project_samples[sample_index]:
-                    project_samples[sample_index]["ms_data_files"] = (
-                        dict_to_df(
-                            project_samples[sample_index]["ms_data_files"]
-                        )
-                    )
-
-            project_samples = dict_to_df(project_samples)
-
-        return project_samples
-
-    def get_analysis_protocols(
-        self,
-        analysis_protocol_name: str = None,
-        analysis_protocol_id: str = None,
-    ):
-        """
-        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.
-
-        Returns
-        -------
-        protocols: list
-            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": ... },
-                ...
-            ]
-
-        >>> 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.
-        """
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        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 = []
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            protocols = s.get(URL, params={"all": "true"})
-            if protocols.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Please check your parameters."
-                )
-            if not analysis_protocol_id and not analysis_protocol_name:
-                res = protocols.json()["data"]
-
-            if analysis_protocol_id and not analysis_protocol_name:
-                res = [protocols.json()]
-
-            if not analysis_protocol_id and analysis_protocol_name:
-                res = [
-                    protocol
-                    for protocol in protocols.json()["data"]
-                    if protocol["analysis_protocol_name"]
-                    == analysis_protocol_name
-                ]
-
-            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
-                    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
-
-    def get_analysis(
-        self,
-        analysis_id: str = None,
-        folder_id: str = None,
-        show_folders=True,
-        analysis_only=True,
-    ):
-        """
-        Returns a list of analyses objects for the authenticated user. If no id is provided, returns all analyses for the authenticated user.
-
-        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, 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.
-
-        Returns
-        -------
-        analyses: dict
-            Contains a list of analyses objects for the authenticated user.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.get_analysis()
-        >>> [
-                {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", ...}]
-        """
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}api/v1/analyses"
-        res = []
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            params = {"all": "true"}
-            if folder_id:
-                params["folder"] = folder_id
-
-            analyses = s.get(
-                f"{URL}/{analysis_id}" if analysis_id else 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"]]
-
-            folders = []
-            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
-                    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_analysis(folder_id=folder)
-
-            if analysis_only:
-                res = [
-                    analysis for analysis in res if not analysis["is_folder"]
-                ]
-            return res
-
-    def get_analysis_result(self, analysis_id: str, download_path: str = ""):
-        """
-        Given an `analysis_id`, this function returns all relevant analysis data files in form of downloadable content, if applicable.
-
-        Parameters
-        ----------
-        analysis_id : str
-            ID of the analysis for which the data is to be fetched.
-
-        download_path : bool
-            String flag denoting where the user wants the files downloaded. Can be local or absolute as long as the path is valid. Defaults to an empty string.
-
-        Returns
-        -------
-        links: dict
-            Contains dataframe objects for the `analysis_id`, given that the analysis has been complete.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-
-        >>> seer_sdk.get_analysis_result("YOUR_ANALYSIS_ID_HERE")
-        >>> {
-                "peptide_np": <peptide_np dataframe object>,
-                "peptide_panel": <peptide_panel dataframe object>,
-                "protein_np": <protein_np dataframe object>,
-                "protein_panel": <protein_panel dataframe object>
-            }
-
-        >>> seer_sdk.get_analysis_result("YOUR_ANALYSIS_ID_HERE", download_path="/Users/Downloads")
-        >>> { "status": "Download complete." }
-        """
-
-        if not analysis_id:
-            raise ValueError("Analysis ID cannot be empty.")
-
-        if download_path and not os.path.exists(download_path):
-            raise ValueError("The download path you entered is invalid.")
-
-        if self.get_analysis(analysis_id)[0]["status"] in ["FAILED", None]:
-            raise ValueError(
-                "Cannot generate links for failed or null analyses."
-            )
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}api/v1/data"
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            protein_data = s.get(
-                f"{URL}/protein?analysisId={analysis_id}&retry=false"
-            )
-
-            if protein_data.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Could not fetch protein data. Please check your parameters."
-                )
-            protein_data = protein_data.json()
-
-            peptide_data = s.get(
-                f"{URL}/peptide?analysisId={analysis_id}&retry=false"
-            )
-
-            if peptide_data.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Could not fetch peptide data. Please check your parameters."
-                )
-
-            peptide_data = peptide_data.json()
-
-            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"]),
-            }
-
-            if download_path:
-                name = f"{download_path}/downloads/{analysis_id}"
-                if not os.path.exists(name):
-                    os.makedirs(name)
-
-                links["peptide_np"].to_csv(f"{name}/peptide_np.csv", sep="\t")
-                links["peptide_panel"].to_csv(
-                    f"{name}/peptide_panel.csv", sep="\t"
-                )
-                links["protein_np"].to_csv(f"{name}/protein_np.csv", sep="\t")
-                links["protein_panel"].to_csv(
-                    f"{name}/protein_panel.csv", sep="\t"
-                )
-
-                return {"status": "Download complete."}
-
-            return links
-
-    def analysis_complete(self, analysis_id: str):
-        """
-        Returns the status of the analysis with the given id.
-
-        Parameters
-        ----------
-        analysis_id : str
-            The analysis id.
-
-        Returns
-        -------
-        res : dict
-            A dictionary containing the status of the analysis.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.analysis_complete("YOUR_ANALYSIS_ID_HERE")
-        >>> {
-                "status": "SUCCEEDED"
-            }
-        """
-
-        if not analysis_id:
-            raise ValueError("Analysis id cannot be empty.")
-
-        try:
-            res = self.get_analysis(analysis_id)
-        except ValueError:
-            return ValueError("Analysis not found. Your ID could be incorrect")
-
-        return {"status": res[0]["status"]}
-
-    def list_ms_data_files(self, folder="", space=None):
-        """
-        Lists all the MS data files in the given folder as long as the folder path passed in the params is valid.
-
-        Parameters
-        ----------
-        folder : str, optional
-            Folder path to list the files from. Defaults to an empty string and displays all files for the user.
-        space : str, optional
-            ID of the user group to which the files belong, defaulted to None.
-
-        Returns
-        -------
-        list
-            Contains the list of files in the folder.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> sdk = SeerSDK()
-        >>> folder_path = "test-may-2/"
-        >>> sdk.list_ms_data_files(folder_path)
-        >>> [
-            "test-may-2/EXP20028/EXP20028_2020ms0096X10_A.raw",
-            "test-may-2/agilent/05_C2_19ug-r001.d.zip",
-            "test-may-2/agilent/08_BC_24ug-r001.d.zip",
-            "test-may-2/d.zip/EXP22023_2022ms0143bX10_A_GA2_1_6681.d/EXP22023_2022ms0143bX10_A_GA2_1_6681.d.zip",
-            "test-may-2/DIA/EXP20002_2020ms0142X10_A.wiff",
-            "test-may-2/DIA/EXP20002_2020ms0142X10_A.wiff.scan",
-            "test-may-2/DIA/EXP20002_2020ms0142X17_A.wiff",
-            "test-may-2/DIA/EXP20002_2020ms0142X17_A.wiff.scan",
-            "test-may-2/DIA/EXP20002_2020ms0142X18_A.wiff",
-            "test-may-2/DIA/EXP20002_2020ms0142X18_A.wiff.scan"
-        ]
-        """
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = (
-            f"{self._auth.url}api/v1/msdataindex/filesinfolder?folder={folder}"
-            if not space
-            else f"{self._auth.url}api/v1/msdataindex/filesinfolder?folder={folder}&userGroupId={space}"
-        )
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            files = s.get(URL)
-
-            if files.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Please check your parameters."
-                )
-            return files.json()["filesList"]
-
-    def download_ms_data_files(
-        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.
-
-        Parameters
-        ----------
-        paths : list[str]
-            List of paths to download.
-        download_path : str
-            Path to download the files to.
-        space : str, optional
-            ID of the user group to which the files belongs, defaulted to None.
-
-        Returns
-        -------
-        message: dict
-            Contains the message whether the files were downloaded or not.
-        """
-
-        urls = []
-
-        if not download_path:
-            download_path = os.getcwd()
-            print(f"\nDownload path not specified.\n")
-
-        if not os.path.isdir(download_path):
-            print(
-                f'\nThe path "{download_path}" you specified does not exist, was either invalid or not absolute.\n'
-            )
-            download_path = f"{os.getcwd()}/downloads"
-
-        name = (
-            download_path if download_path[-1] != "/" else download_path[:-1]
-        )
-
-        if not os.path.exists(name):
-            os.makedirs(name)
-
-        print(f'Downloading files to "{name}"\n')
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}api/v1/msdataindex/download/getUrl"
-        tenant_id = jwt.decode(ID_TOKEN, options={"verify_signature": False})[
-            "custom:tenantId"
-        ]
-
-        for path in paths:
-            with requests.Session() as s:
-                s.headers.update(HEADERS)
-
-                download_url = s.post(
-                    URL,
-                    json={
-                        "filepath": f"{tenant_id}/{path}",
-                        "userGroupId": space,
-                    },
-                )
-
-                if download_url.status_code != 200:
-                    raise ValueError(
-                        "Could not download file. Please check if the backend is running."
-                    )
-                urls.append(download_url.text)
-
-        for i in range(len(urls)):
-            filename = paths[i].split("/")[-1]
-            url = urls[i]
-
-            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"{name}/{filename}",
-                            reporthook=download_hook(t),
-                            data=None,
-                        )
-                        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}/")
-
-            else:
-                raise ValueError(
-                    "Your download failed. Please check if the backend is still running."
-                )
-
-            print(f"Finished downloading {filename}\n")
-
-        return {"message": f"Files downloaded successfully to '{name}'"}
-
-    def group_analysis_results(self, analysis_id: str, box_plot: dict = None):
-        """
-        Returns the group analysis data for the given analysis id, provided it exists.
-
-        Parameters
-        ----------
-        analysis_id : str
-            The analysis id.
-
-        box_plot : dict, optional
-            The box plot configuration needed for the analysis, defaulted to None. Contains `feature_type` ("protein" or "peptide") and `feature_ids` (comma separated list of feature IDs) keys.
-
-        Returns
-        -------
-        res : dict
-            A dictionary containing the group analysis data.
-
-        Examples
-        -------
-        >>> from seer_pas_sdk import SeerSDK
-        >>> seer_sdk = SeerSDK()
-        >>> seer_sdk.group_analysis_results("YOUR_ANALYSIS_ID_HERE")
-        >>> {
-                "pre": {
-                    "protein": [],
-                    "peptide": [],
-                },
-                "post": {
-                    "protein": {},
-                    "protein_url": {
-                        "protein_processed_file_url": "",
-                        "protein_processed_long_form_file_url": "",
-                    },
-                    "peptide": {},
-                    "peptide_url": {
-                        "peptide_processed_file_url": "",
-                        "peptide_processed_long_form_file_url": "",
-                    },
-                },
-                "box_plot": []
-            }
-        """
-
-        if not analysis_id:
-            raise ValueError("Analysis ID cannot be empty.")
-
-        ID_TOKEN, ACCESS_TOKEN = self._auth.get_token()
-        HEADERS = {
-            "Authorization": f"{ID_TOKEN}",
-            "access-token": f"{ACCESS_TOKEN}",
-        }
-        URL = f"{self._auth.url}"
-
-        res = {
-            "pre": {
-                "protein": [],
-                "peptide": [],
-            },
-            "post": {
-                "protein": {},
-                "protein_url": {
-                    "protein_processed_file_url": "",
-                    "protein_processed_long_form_file_url": "",
-                },
-                "peptide": {},
-                "peptide_url": {
-                    "peptide_processed_file_url": "",
-                    "peptide_processed_long_form_file_url": "",
-                },
-            },
-            "box_plot": [],
-        }
-
-        # Pre-GA data call
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            protein_pre_data = s.post(
-                url=f"{URL}api/v2/groupanalysis/protein",
-                json={"analysisId": analysis_id, "grouping": "condition"},
-            )
-            if protein_pre_data.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Could not fetch group analysis protein pre data. Please check your parameters."
-                )
-
-            protein_pre_data = protein_pre_data.json()
-
-            res["pre"]["protein"] = protein_pre_data
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            peptide_pre_data = s.post(
-                url=f"{URL}api/v2/groupanalysis/peptide",
-                json={"analysisId": analysis_id, "grouping": "condition"},
-            )
-            if peptide_pre_data.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Could not fetch group analysis peptide pre data. Please check your parameters."
-                )
-
-            peptide_pre_data = peptide_pre_data.json()
-            res["pre"]["peptide"] = peptide_pre_data
-
-        # Post-GA data call
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-
-            get_saved_result = s.get(
-                f"{URL}api/v1/groupanalysis/getSavedResults?analysisid={analysis_id}"
-            )
-
-            if get_saved_result.status_code != 200:
-                raise ValueError(
-                    "Invalid request. Could not fetch group analysis post data. Please check your parameters."
-                )
-            get_saved_result = get_saved_result.json()
-
-            # Protein data
-            if "pgResult" in get_saved_result:
-                res["post"]["protein"] = get_saved_result["pgResult"]
-
-            # Peptide data
-            if "peptideResult" in get_saved_result:
-                res["post"]["peptide"] = get_saved_result["peptideResult"]
-
-            # Protein URLs
-            if "pgProcessedFileUrl" in get_saved_result:
-                res["post"]["protein_url"]["protein_processed_file_url"] = (
-                    get_saved_result["pgProcessedFileUrl"]
-                )
-            if "pgProcessedLongFormFileUrl" in get_saved_result:
-                res["post"]["protein_url"][
-                    "protein_processed_long_form_file_url"
-                ] = get_saved_result["pgProcessedLongFormFileUrl"]
-
-            # Peptide URLs
-            if "peptideProcessedFileUrl" in get_saved_result:
-                res["post"]["peptide_url"]["peptide_processed_file_url"] = (
-                    get_saved_result["peptideProcessedFileUrl"]
-                )
-
-            if "peptideProcessedLongFormFileUrl" in get_saved_result:
-                res["post"]["peptide_url"][
-                    "peptide_processed_long_form_file_url"
-                ] = get_saved_result["peptideProcessedLongFormFileUrl"]
-
-        # Box plot data call
-        if not box_plot:
-            del res["box_plot"]
-            return res
-
-        with requests.Session() as s:
-            s.headers.update(HEADERS)
-            box_plot["feature_type"] = box_plot["feature_type"].lower()
-            box_plot_data = s.post(
-                url=f"{URL}api/v1/groupanalysis/rawdata",
-                json={
-                    "analysisId": analysis_id,
-                    "featureIds": (
-                        ",".join(box_plot["feature_ids"])
-                        if len(box_plot["feature_ids"]) > 1
-                        else box_plot["feature_ids"][0]
-                    ),
-                    "featureType": f"{box_plot['feature_type']}group",
-                },
-            )
-            if box_plot_data.status_code != 200:
-                raise ValueError(
-                    "Invalid request, could not fetch box plot data. Please verify your 'box_plot' parameters, including 'feature_ids' (comma-separated list of feature IDs) and 'feature_type' (needs to be a either 'protein' or 'peptide')."
-                )
-
-            box_plot_data = box_plot_data.json()
-            res["box_plot"] = box_plot_data
-
-        return res
+from .sdk import SeerSDK