seer-pas-sdk 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

seer_pas_sdk/core/__init__.py

@@ -20,7 +20,7 @@ class SeerSDK:
 
     Examples
     -------
-    >>> from core import SeerSDK
+    >>> from seer_pas_sdk import SeerSDK
     >>> USERNAME = "test"
     >>> PASSWORD = "test-password"
     >>> INSTANCE = "EU"
@@ -51,7 +51,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> seer_sdk.get_spaces()
         >>> [
@@ -97,7 +97,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> seer_sdk.get_plate_metadata()
         >>> [
@@ -170,7 +170,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> seer_sdk.get_project_metadata()
         >>> [
@@ -263,17 +263,17 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
 
-        >>> seer_sdk.get_samples_metadata(plate_id="7ec8cad0-15e0-11ee-bdf1-bbaa73585acf")
+        >>> seer_sdk._get_samples_metadata(plate_id="7ec8cad0-15e0-11ee-bdf1-bbaa73585acf")
         >>> [
                 { "id": ... },
                 { "id": ... },
                 ...
             ]
 
-        >>> seer_sdk.get_samples_metadata(df=True)
+        >>> seer_sdk._get_samples_metadata(df=True)
         >>>                                     id  ...      control
         0     812139c0-15e0-11ee-bdf1-bbaa73585acf  ...
         1     803e05b0-15e0-11ee-bdf1-bbaa73585acf  ...  MPE Control
@@ -332,7 +332,46 @@ class SeerSDK:
             for entry in res:
                 del entry["tenant_id"]
 
-        return res if not df else dict_to_df(res)
+        # 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):
         """
@@ -354,7 +393,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> sample_ids = ["812139c0-15e0-11ee-bdf1-bbaa73585acf", "803e05b0-15e0-11ee-bdf1-bbaa73585acf"]
 
@@ -425,7 +464,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> plate_id = "7ec8cad0-15e0-11ee-bdf1-bbaa73585acf"
 
@@ -442,7 +481,7 @@ class SeerSDK:
 
             [2 rows x 26 columns]
         """
-        plate_samples = self.get_samples_metadata(plate_id=plate_id)
+        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)
 
@@ -470,7 +509,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> project_id = "7e48e150-8a47-11ed-b382-bf440acece26"
 
@@ -549,7 +588,7 @@ class SeerSDK:
             return ValueError("No project ID specified.")
 
         sample_ids = []
-        project_samples = self.get_samples_metadata(
+        project_samples = self._get_samples_metadata(
             project_id=project_id, df=False
         )
 
@@ -610,7 +649,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> seer_sdk.get_analysis_protocols()
         >>> [
@@ -678,7 +717,13 @@ class SeerSDK:
 
             return res
 
-    def get_analysis(self, analysis_id: str = None):
+    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.
 
@@ -687,6 +732,17 @@ class SeerSDK:
         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
@@ -694,7 +750,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> seer_sdk.get_analysis()
         >>> [
@@ -718,10 +774,14 @@ class SeerSDK:
         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={"all": "true"},
+                f"{URL}/{analysis_id}" if analysis_id else URL, params=params
             )
+
             if analyses.status_code != 200:
                 raise ValueError(
                     "Invalid request. Please check your parameters."
@@ -732,6 +792,7 @@ class SeerSDK:
             else:
                 res = [analyses.json()["analysis"]]
 
+            folders = []
             for entry in range(len(res)):
                 if "tenant_id" in res[entry]:
                     del res[entry]["tenant_id"]
@@ -739,10 +800,27 @@ class SeerSDK:
                 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 = ""):
@@ -764,7 +842,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
 
         >>> seer_sdk.get_analysis_result("YOUR_ANALYSIS_ID_HERE")
@@ -862,7 +940,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> seer_sdk.analysis_complete("YOUR_ANALYSIS_ID_HERE")
         >>> {
@@ -898,7 +976,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> sdk = SeerSDK()
         >>> folder_path = "test-may-2/"
         >>> sdk.list_ms_data_files(folder_path)
@@ -1069,7 +1147,7 @@ class SeerSDK:
 
         Examples
         -------
-        >>> from core import SeerSDK
+        >>> from seer_pas_sdk import SeerSDK
         >>> seer_sdk = SeerSDK()
         >>> seer_sdk.group_analysis_results("YOUR_ANALYSIS_ID_HERE")
         >>> {

{seer_pas_sdk-0.1.0.dist-info → seer_pas_sdk-0.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: seer-pas-sdk
-Version: 0.1.0
+Version: 0.1.2
 Summary: SDK for Seer Proteograph Analysis Suite (PAS)
 Home-page: https://github.com/seerbio/seer-pas-sdk
 Author: Agam Jolly
@@ -12,13 +12,14 @@ Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
 License-File: LICENSE.txt
-Requires-Dist: boto3 ==1.26.152
-Requires-Dist: botocore ==1.29.152
-Requires-Dist: pandas ==2.0.1
-Requires-Dist: PyJWT ==2.8.0
-Requires-Dist: python-dotenv ==1.0.0
-Requires-Dist: Requests ==2.31.0
-Requires-Dist: tqdm ==4.65.0
+Requires-Dist: boto3==1.26.152
+Requires-Dist: botocore==1.29.152
+Requires-Dist: pandas==2.0.1
+Requires-Dist: numpy<2.0.0,>=1.5.3
+Requires-Dist: PyJWT==2.8.0
+Requires-Dist: python-dotenv==1.0.0
+Requires-Dist: Requests==2.31.0
+Requires-Dist: tqdm==4.65.0
 
 # Seer PAS Python SDK
 
@@ -32,3 +33,18 @@ This SDK permits interaction with the Seer Proteograph Analysis Suite using Pyth
 ```shell
 pip install seer-pas-sdk
 ```
+
+## Usage
+
+To import and set up the SDK:
+
+```python
+from seer_pas_sdk import SeerSDK
+
+# Instantiate an SDK object with your credentials:
+sdk = SeerSDK(USERNAME, PASSWORD)
+```
+
+You can then use the SDK's functions to create, query, or retrieve projects, plates, samples, and analyses.
+
+For complete documentation of this SDK, visit [https://seerbio.github.io/seer-pas-sdk/](https://seerbio.github.io/seer-pas-sdk/ "Documentation").

{seer_pas_sdk-0.1.0.dist-info → seer_pas_sdk-0.1.2.dist-info}/RECORD

@@ -1,7 +1,7 @@
 seer_pas_sdk/__init__.py,sha256=Ie6atdmdBV-OmdHHXjhrGhdFGXiyP3JKhKrr3hyvSsA,563
 seer_pas_sdk/auth/__init__.py,sha256=DZcbkYel11GvIn-iiutt9UOVfj9URZ_f89QMHhyGfRg,2277
 seer_pas_sdk/common/__init__.py,sha256=QnBup2dT6okt62Yjdhik4DmLf36Ozgv6KybdvFAULaA,12260
-seer_pas_sdk/core/__init__.py,sha256=Jp0xpFbVLXUt7Zyx8zuMiPacNUYW0Q0VwEFpVmFcuXs,44914
+seer_pas_sdk/core/__init__.py,sha256=J8dAiYsvNbc11zN1mgp7KqjHSVPw9CVwI-uc85UHw5s,47488
 seer_pas_sdk/objects/__init__.py,sha256=DosquJu2-XvDjVj4JFKoXa0DBVS8OroYCDeS5Np4U8Q,3693
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/conftest.py,sha256=nu5Qu8CHwgJEwFpLQ0iX8e5csz4HGIC2oe50AdkA2Ms,317
@@ -9,8 +9,8 @@ tests/test_auth.py,sha256=np4XXbEzoSFf-zXKaZQFL4Ry1ehMtjbXtHG3J6D-zzc,933
 tests/test_common.py,sha256=3VgHPbeLVJCh8V0kBGMvkhTKMd6sN_eLJF3AgvbyH0I,3433
 tests/test_objects.py,sha256=BcQtE8CbGUAnFlbkwsaJalUV6D8WbdwN2aWiQddh3k4,2521
 tests/test_sdk.py,sha256=ZNfsRAe_YHIXfteVugfkcds_lmYb0emIfDbJz7jpqR4,239
-seer_pas_sdk-0.1.0.dist-info/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
-seer_pas_sdk-0.1.0.dist-info/METADATA,sha256=6-Q3axM4k5TbhQptHyFBe-1WEPgV8r5a6yr1tYjvkVc,1257
-seer_pas_sdk-0.1.0.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-seer_pas_sdk-0.1.0.dist-info/top_level.txt,sha256=gMffZ5LfTF87Sr-oiyl-rtY6omfBslYCA2S4DM7YNC8,19
-seer_pas_sdk-0.1.0.dist-info/RECORD,,
+seer_pas_sdk-0.1.2.dist-info/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
+seer_pas_sdk-0.1.2.dist-info/METADATA,sha256=VuuOZGQuA6LaN6MgYSZEHKBJXKRuVZxXNDFLLM63shk,1716
+seer_pas_sdk-0.1.2.dist-info/WHEEL,sha256=Mdi9PDNwEZptOjTlUcAth7XJDFtKrHYaQMPulZeBCiQ,91
+seer_pas_sdk-0.1.2.dist-info/top_level.txt,sha256=gMffZ5LfTF87Sr-oiyl-rtY6omfBslYCA2S4DM7YNC8,19
+seer_pas_sdk-0.1.2.dist-info/RECORD,,

{seer_pas_sdk-0.1.0.dist-info → seer_pas_sdk-0.1.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (73.0.1)
 Root-Is-Purelib: true
 Tag: py3-none-any