seer-pas-sdk 0.1.2__py3-none-any.whl → 0.1.3__py3-none-any.whl

seer_pas_sdk/core/sdk.py

@@ -0,0 +1,1250 @@
+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_auth_headers(self):
+        id_token, access_token = self._auth.get_token()
+        return {
+            "Authorization": id_token,
+            "access-token": access_token,
+        }
+
+    def _get_auth_session(self):
+        sess = requests.Session()
+
+        sess.headers.update(self._get_auth_headers())
+
+        return sess
+
+    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": ... },
+                ...
+            ]
+        """
+
+        URL = f"{self._auth.url}api/v1/usergroups"
+
+        with self._get_auth_session() as s:
+            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": ... }]
+        """
+
+        URL = f"{self._auth.url}api/v1/plates"
+        res = []
+
+        with self._get_auth_session() as s:
+
+            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": ... }]
+        """
+
+        URL = (
+            f"{self._auth.url}api/v1/projects"
+            if not project_id
+            else f"{self._auth.url}api/v1/projects/{project_id}"
+        )
+        res = []
+
+        with self._get_auth_session() as s:
+
+            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 = []
+        URL = f"{self._auth.url}api/v1/samples"
+        sample_params = {"all": "true"}
+
+        with self._get_auth_session() as s:
+
+            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.
+        """
+        URL = f"{self._auth.url}api/v1/samplefields"
+
+        with self._get_auth_session() as s:
+
+            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]
+        """
+
+        URL = f"{self._auth.url}api/v1/msdatas/items"
+
+        res = []
+        for sample_id in sample_ids:
+
+            with self._get_auth_session() as s:
+
+                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.
+        """
+
+        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 self._get_auth_session() as s:
+
+            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", ...}]
+        """
+
+        URL = f"{self._auth.url}api/v1/analyses"
+        res = []
+
+        with self._get_auth_session() as s:
+
+            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."
+            )
+
+        URL = f"{self._auth.url}api/v1/data"
+
+        with self._get_auth_session() as s:
+
+            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"
+        ]
+        """
+
+        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 self._get_auth_session() as s:
+
+            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')
+
+        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 self._get_auth_session() as s:
+
+                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.")
+
+        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 self._get_auth_session() as s:
+
+            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