seer-pas-sdk 0.3.2__py3-none-any.whl → 0.3.4__py3-none-any.whl

seer_pas_sdk/core/sdk.py

@@ -515,6 +515,8 @@ class SeerSDK:
                     f"Failed to fetch sample data for plate ID: {plate_id}."
                 )
             res = samples.json()["data"]
+            if not res:
+                return [] if not as_df else dict_to_df(res)
             res_df = dict_to_df(res)
 
             # API returns empty strings if not a control, replace with None for filtering purposes
@@ -1195,7 +1197,9 @@ class SeerSDK:
 
             return peptide_data
 
-    def list_search_result_files(self, analysis_id: str):
+    def list_search_result_files(
+        self, analysis_id: str, folder: str = None, recursive: bool = False
+    ):
         """
         Given an analysis id, this function returns a list of files associated with the analysis.
 
@@ -1204,6 +1208,12 @@ class SeerSDK:
         analysis_id : str
             ID of the analysis for which the data is to be fetched.
 
+        folder : str, optional
+            Root folder key to list search result files from, defaulted to None.
+
+        recursive : bool, optional
+            Whether to list files recursively from subfolders, defaulted to False.
+
         Returns
         -------
         files: list[str]
@@ -1218,9 +1228,15 @@ class SeerSDK:
 
         if analysis_metadata.get("status") in ["Failed", None]:
             raise ValueError("Cannot find files for a failed analysis.")
+
+        params = {"all": "true"}
+        if folder:
+            params["folderKey"] = folder
+
         with self._get_auth_session() as s:
             response = s.get(
-                f"{self._auth.url}api/v2/analysisResultFiles/{analysis_id}"
+                f"{self._auth.url}api/v2/analysisResultFiles/{analysis_id}",
+                params=params,
             )
             if response.status_code != 200:
                 raise ServerError(
@@ -1228,8 +1244,25 @@ class SeerSDK:
                 )
             response = response.json()
             files = []
+            folders = []
             for row in response["data"]:
-                files.append(row["filename"])
+                if folder:
+                    row["filename"] = f"{folder}/{row['filename']}"
+                if row["isFolder"]:
+                    if recursive:
+                        folders.append(row["filename"])
+                    else:
+                        row["filename"] += "/"
+                        files.append(row["filename"])
+                else:
+                    files.append(row["filename"])
+
+            if recursive:
+                for subfolder in folders:
+                    files += self.list_search_result_files(
+                        analysis_id, folder=subfolder, recursive=recursive
+                    )
+
             return files
 
     def get_search_result(
@@ -1737,7 +1770,32 @@ class SeerSDK:
                 raise ServerError(
                     "Could not fetch protein results table. Please verify that your analysis completed."
                 )
-            return dict_to_df(res.json()) if as_df else res.json()
+            res = dict_to_df(res.json())
+            res.rename(
+                columns={
+                    "proteinId": "uniprot_id",
+                    "n": "n_samples",
+                    "bp": "biological_process",
+                    "mf": "molecular_function",
+                    "cc": "cellular_component",
+                    "nFrac": "fraction_samples",
+                    "proteinNames": "protein_name",
+                    "geneName": "gene_name",
+                },
+                inplace=True,
+            )
+
+            res.drop(
+                columns=[
+                    "median_undefined",
+                    "n_undefined",
+                    "n_null",
+                    "median_null",
+                ],
+                inplace=True,
+                errors="ignore",
+            )
+            return res if as_df else res.to_dict(orient="records")
 
     def get_peptide_results_table(
         self,
@@ -1779,9 +1837,28 @@ class SeerSDK:
             )
             if res.status_code != 200:
                 raise ServerError(
-                    "Could not fetch protein results table. Please verify that your analysis completed."
+                    "Could not fetch peptide results table. Please verify that your analysis completed."
                 )
-            return dict_to_df(res.json()) if as_df else res.json()
+            res = dict_to_df(res.json())
+            res.rename(
+                columns={
+                    "proteinId": "uniprot_id",
+                    "n": "n_samples",
+                    "bp": "biological_process",
+                    "mf": "molecular_function",
+                    "cc": "cellular_component",
+                    "nFrac": "fraction_samples",
+                    "proteinNames": "protein_name",
+                    "geneName": "gene_name",
+                },
+                inplace=True,
+            )
+
+            res.drop(columns=["n_undefined"], inplace=True, errors="ignore")
+            res.drop(
+                columns=["median_undefined"], inplace=True, errors="ignore"
+            )
+            return res if as_df else res.to_dict(orient="records")
 
     def list_ms_data_files(self, folder="", space=None):
         """

{seer_pas_sdk-0.3.2.dist-info → seer_pas_sdk-0.3.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: seer-pas-sdk
-Version: 0.3.2
+Version: 0.3.4
 Summary: SDK for Seer Proteograph Analysis Suite (PAS)
 Author-email: Ryan Sun <rsun@seer.bio>
 License: 

{seer_pas_sdk-0.3.2.dist-info → seer_pas_sdk-0.3.4.dist-info}/RECORD

@@ -5,14 +5,14 @@ seer_pas_sdk/common/__init__.py,sha256=jA5qm-t9x3qXMp5Q6v7vV2kZdLw32-lnbtf0fPY4l
 seer_pas_sdk/common/errors.py,sha256=4HFORWnaQQCMXRE8kwdsJWvQRB_3KFEZ7yMb391e4gA,142
 seer_pas_sdk/common/groupanalysis.py,sha256=DxB-gbQfYzl7p9MTYWDIqghcH-IeakzdYdrRZrlIHek,1730
 seer_pas_sdk/core/__init__.py,sha256=rxbKgg-Qe24OaxX2zyHHYPYgDCTEKE_-41bB2wvpvL4,25
-seer_pas_sdk/core/sdk.py,sha256=P8t_QNS8YmwBhdTtkbW02RhzN0Mb2u9F92JAOqvvmUg,105847
+seer_pas_sdk/core/sdk.py,sha256=NHhUCxuhea_KhCd3FLpojCwkOZDIZuvjU7K52h695KY,108508
 seer_pas_sdk/core/unsupported.py,sha256=XAPZ3tidqjnsgftf3NUdTGIzvnsjHy0e_eGRCAo6GPo,59890
 seer_pas_sdk/objects/__init__.py,sha256=HJLS6sOr7DfzdI14fv5dWcITEj5QQsKcdfED3YNvUrY,107
 seer_pas_sdk/objects/groupanalysis.py,sha256=x3D_5NmYBoPDilNCQqUoCFARIfIeUq4FBY3_N6u8tfM,994
 seer_pas_sdk/objects/platemap.py,sha256=8IvJPAecs_e_FyqibzhCw-O4zjCFnf-zMUp_5krTEsg,5864
 seer_pas_sdk/objects/volcanoplot.py,sha256=tKuCWDIdoO8FLJlhpXhuwHn0aMYnvudTugxAslDXyGs,9357
-seer_pas_sdk-0.3.2.dist-info/licenses/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
-seer_pas_sdk-0.3.2.dist-info/METADATA,sha256=WZECPlPd8k2mEgEznlhfXqYbbMHbdOZn8q2D51B4blo,13448
-seer_pas_sdk-0.3.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-seer_pas_sdk-0.3.2.dist-info/top_level.txt,sha256=-2kZ-KFMGtXwr8H1O5llMKlcJ8gRKohEmrIvazXB61s,13
-seer_pas_sdk-0.3.2.dist-info/RECORD,,
+seer_pas_sdk-0.3.4.dist-info/licenses/LICENSE.txt,sha256=DVQuDIgE45qn836wDaWnYhSdxoLXgpRRKH4RuTjpRZQ,10174
+seer_pas_sdk-0.3.4.dist-info/METADATA,sha256=QuSAislG3NV9SE66n1xNF4Kf7Nk704jSEPCyefSoP_E,13448
+seer_pas_sdk-0.3.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+seer_pas_sdk-0.3.4.dist-info/top_level.txt,sha256=-2kZ-KFMGtXwr8H1O5llMKlcJ8gRKohEmrIvazXB61s,13
+seer_pas_sdk-0.3.4.dist-info/RECORD,,