polly-python 4.2.0__tar.gz → 4.4.0__tar.gz

{polly_python-4.2.0/polly_python.egg-info → polly_python-4.4.0}/PKG-INFO

@@ -1,36 +1,47 @@
 Metadata-Version: 2.4
 Name: polly_python
-Version: 4.2.0
+Version: 4.4.0
 Summary: Polly SDK
 Home-page: https://github.com/ElucidataInc/polly-python
 Project-URL: Documentation, https://docs.elucidata.io
 Project-URL: Tutorial Notebooks, https://github.com/ElucidataInc/polly-python
-Requires-Python: <3.12,>=3.9
+Requires-Python: <3.15,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: cmapPy<=4.0.1
-Requires-Dist: cloudpathlib>=0.15.0
+Requires-Dist: cmapPy==4.0.1
+Requires-Dist: cloudpathlib<1.0.0,>=0.19.0
 Requires-Dist: retrying==1.3.4
 Requires-Dist: rst2txt==1.1.0
-Requires-Dist: python-jose==3.3.0
-Requires-Dist: mixpanel==4.10.0
-Requires-Dist: Deprecated>=1.2.12
-Requires-Dist: pytest>=6.2.5
-Requires-Dist: cryptography<=38.0.0,>=37.0.1
-Requires-Dist: plotly>=5.0.0; python_version >= "3.7"
-Requires-Dist: pandas<=2.2.2,>=1.3.5; python_version >= "3.7"
-Requires-Dist: numpy<=1.26.4
-Requires-Dist: pydantic==1.10.12; python_version >= "3.7"
-Requires-Dist: requests==2.28.1
-Requires-Dist: boto3<2.0,>=1.24.0; python_version >= "3.7"
-Requires-Dist: botocore<2.0,>=1.27.0; python_version >= "3.7"
-Requires-Dist: joblib>=1.2.0; python_version >= "3.7"
-Requires-Dist: tabulate==0.9.0
-Requires-Dist: tqdm==4.65.0; python_version >= "3.7"
+Requires-Dist: mixpanel<5.0.0,>=4.10.0
+Requires-Dist: Deprecated<2.0.0,>=1.2.12
+Requires-Dist: pydantic<3.0.0,>=2.8.2
+Requires-Dist: requests<=2.32.3,>=2.31.0
+Requires-Dist: boto3<2.0.0,>=1.34.0
+Requires-Dist: joblib==1.4.2
+Requires-Dist: rich<14.0.0,>=13.0.0
+Requires-Dist: tqdm==4.66.4
+Requires-Dist: plotly==6.3.1
+Requires-Dist: cryptography<=38.0.0; python_full_version >= "3.9.0" and python_full_version <= "3.9.1"
+Requires-Dist: cryptography==46.0.2; python_full_version >= "3.9.2"
+Requires-Dist: setuptools>=65.0.0; python_version >= "3.12"
+Requires-Dist: pandas<=2.2.3,>=1.5.3; python_version == "3.9"
+Requires-Dist: pandas<=2.2.3,>=1.5.3; python_version == "3.10"
+Requires-Dist: pandas<=2.2.3,>=1.5.3; python_version == "3.11"
+Requires-Dist: pandas<=2.2.3,>=2.1.0; python_version == "3.12"
+Requires-Dist: pandas<=2.2.3,>=2.2.2; python_version == "3.13"
+Requires-Dist: pandas<=2.2.3,>=2.2.2; python_version == "3.14"
+Requires-Dist: numpy<=1.25.2,>=1.23.0; python_version == "3.9"
+Requires-Dist: numpy<=2.2.2,>=1.23.0; python_version == "3.10"
+Requires-Dist: numpy<=2.2.2,>=1.24.0; python_version == "3.11"
+Requires-Dist: numpy<=2.2.2,>=1.26.0; python_version == "3.12"
+Requires-Dist: numpy<=2.2.2,>=2.2.0; python_version == "3.13"
+Requires-Dist: numpy<=2.2.2,>=2.2.0; python_version == "3.14"
 Provides-Extra: testing
 Requires-Dist: black; extra == "testing"
 Requires-Dist: flake8; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-mock; extra == "testing"
+Requires-Dist: moto; extra == "testing"
 Dynamic: license-file
 
 [![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)

polly_python-4.4.0/polly/__init__.py

@@ -0,0 +1 @@
+__version__ = "4.4.0"

{polly_python-4.2.0 → polly_python-4.4.0}/polly/analyze.py

@@ -272,12 +272,12 @@ class Analyze:
         )
 
         cohort_df["kw_condition"] = "NA"
-        cohort_df.loc[
-            cohort_df["sample_id"].isin(control_ids), "kw_condition"
-        ] = "control"
-        cohort_df.loc[
-            cohort_df["sample_id"].isin(perturbation_ids), "kw_condition"
-        ] = "perturbation"
+        cohort_df.loc[cohort_df["sample_id"].isin(control_ids), "kw_condition"] = (
+            "control"
+        )
+        cohort_df.loc[cohort_df["sample_id"].isin(perturbation_ids), "kw_condition"] = (
+            "perturbation"
+        )
 
         return cohort_df
 

{polly_python-4.2.0 → polly_python-4.4.0}/polly/helpers.py

@@ -196,7 +196,7 @@ def upload_to_S3(cloud_path: str, local_path: str, credentials: dict) -> None:
                 and path_split[len(path_split) - 1][0] in punctuation_chars
             ):
                 raise InvalidParameterException(
-                    f"path can't start with {path_split[len(path_split)-1][0]}"
+                    f"path can't start with {path_split[len(path_split) - 1][0]}"
                 )
             new_source_path = client.CloudPath(cloud_path)
             if new_source_path.exists():
@@ -245,7 +245,7 @@ def download_from_S3(
             # If copy_workspace_path is True, append workspace_path to destination_path to copy the directory structure.
             # ex- make_path('/home/user/project/', 'folder1/folder2') = '/home/user/project/folder1/folder2'
             if copy_workspace_path is True:
-                destination_path = f"{make_path(destination_path,workspace_path)}"
+                destination_path = f"{make_path(destination_path, workspace_path)}"
 
             source_path.copytree(destination_path, force_overwrite_to_cloud=True)
         except ClientError as e:

{polly_python-4.2.0 → polly_python-4.4.0}/polly/omixatlas.py

@@ -1060,10 +1060,10 @@ class OmixAtlas:
             )
 
         frontendinfo_curr_data = repo_curr_data["data"]["attributes"]["frontend_info"]
-        repo_curr_data["data"]["attributes"][
-            "frontend_info"
-        ] = omix_hlpr.update_frontendinfo_value(
-            frontendinfo_curr_data, image_url, description, display_name, controls
+        repo_curr_data["data"]["attributes"]["frontend_info"] = (
+            omix_hlpr.update_frontendinfo_value(
+                frontendinfo_curr_data, image_url, description, display_name, controls
+            )
         )
 
         repository_url = f"{self.resource_url}/{repo_key}"

{polly_python-4.2.0 → polly_python-4.4.0}/polly/polly_kg.py

@@ -277,13 +277,30 @@ class PollyKG:
                 result_json = requests.get(result_s3_signed_url)
                 return result_json.json()
             elif status == "FAILED":
-                raise QueryFailedException(
+                metadata = (
                     status_response.json()
                     .get("data", {})
                     .get("attributes", {})
                     .get("metadata", {})
-                    .get("error")
                 )
+                # Try new format first: metadata.results.error and metadata.results.details
+                results = metadata.get("results", {})
+                if results and ("error" in results or "details" in results):
+                    error_type = results.get("error", "Unknown error")
+                    error_details = results.get("details", "")
+                    error_message = (
+                        f"{error_type}: {error_details}"
+                        if error_details
+                        else error_type
+                    )
+                else:
+                    # Fallback to old format: metadata.error
+                    error_message = metadata.get(
+                        "error", "Query failed without a specific error message."
+                    )
+
+                print(f"Query failed. Query ID: {query_id}. Error: {error_message}")
+                raise QueryFailedException(error_message)
         except Exception as e:
             print(e)
             raise e
@@ -386,11 +403,25 @@ class PollyKG:
 
             status = data.get("attributes", {}).get("status")
             if status == "FAILED":
-                raise QueryFailedException(
-                    data.get("attributes", {})
-                    .get("metadata", {})
-                    .get("error", "Query failed without a specific error message.")
-                )
+                metadata = data.get("attributes", {}).get("metadata", {})
+                # Try new format first: metadata.results.error and metadata.results.details
+                results = metadata.get("results", {})
+                if results and ("error" in results or "details" in results):
+                    error_type = results.get("error", "Unknown error")
+                    error_details = results.get("details", "")
+                    error_message = (
+                        f"{error_type}: {error_details}"
+                        if error_details
+                        else error_type
+                    )
+                else:
+                    # Fallback to old format: metadata.error
+                    error_message = metadata.get(
+                        "error", "Query failed without a specific error message."
+                    )
+
+                print(f"Query failed. Query ID: {query_id}. Error: {error_message}")
+                raise QueryFailedException(error_message)
             result_s3_signed_url = (
                 data.get("attributes", {})
                 .get("metadata", {})
@@ -436,11 +467,25 @@ class PollyKG:
 
             status = data.get("attributes", {}).get("status")
             if status == "FAILED":
-                raise QueryFailedException(
-                    data.get("attributes", {})
-                    .get("metadata", {})
-                    .get("error", "Query failed without a specific error message.")
-                )
+                metadata = data.get("attributes", {}).get("metadata", {})
+                # Try new format first: metadata.results.error and metadata.results.details
+                results = metadata.get("results", {})
+                if results and ("error" in results or "details" in results):
+                    error_type = results.get("error", "Unknown error")
+                    error_details = results.get("details", "")
+                    error_message = (
+                        f"{error_type}: {error_details}"
+                        if error_details
+                        else error_type
+                    )
+                else:
+                    # Fallback to old format: metadata.error
+                    error_message = metadata.get(
+                        "error", "Query failed without a specific error message."
+                    )
+
+                print(f"Query failed. Query ID: {query_id}. Error: {error_message}")
+                raise QueryFailedException(error_message)
             result_s3_signed_url = (
                 data.get("attributes", {})
                 .get("metadata", {})
@@ -503,3 +548,92 @@ class PollyKG:
             return handle_success_and_error_response(response)
         except Exception as e:
             print(e)
+
+    @Track.track_decorator
+    def get_all_kgs(
+        self,
+        include_unpublished: bool = False,
+        include_instances: bool = False,
+        include_terminated: bool = False,
+    ) -> list:
+        """Retrieve all available Knowledge Graphs.
+
+        This function fetches a list of all available Knowledge Graphs (KGs)
+        that the user has access to, including their metadata such as kg_id,
+        kg_name, kg_description, version_id, created_at timestamp, and
+        published status.
+
+        Args:
+            include_unpublished (bool, optional): Include unpublished knowledge graphs.
+                Defaults to False.
+            include_instances (bool, optional): Include instance information for each KG.
+                When True, each KG will include an 'instances' array with details about
+                available instances (instance_id, instance_type, CPU/RAM, etc.).
+                Defaults to False.
+            include_terminated (bool, optional): Include terminated instances in the response.
+                Only applies when include_instances is True. Defaults to False.
+
+        Returns:
+            list: A list of dictionaries, where each dictionary contains:
+                - kg_id (str): Unique identifier for the knowledge graph
+                - kg_name (str): Name of the knowledge graph
+                - kg_description (str): Description of the knowledge graph
+                - version_id (int): Current version ID
+                - created_at (int): Creation timestamp (Unix epoch in milliseconds)
+                - published (bool): Whether the KG is published
+                - instances (list, optional): Available when include_instances=True.
+                  Each instance contains:
+                    - instance_id (str): Unique identifier for the instance
+                    - instance_type (str): Type/size of instance (e.g., "t3.medium")
+                    - is_terminated (bool): Whether the instance is terminated
+                    - default_instance (bool): Whether this is the default instance
+                    - org_id (int): Organization ID
+                    - created_at (int): Instance creation timestamp
+
+        Raises:
+            ResourceNotFoundError: Raised when no knowledge graphs are found.
+            AccessDeniedError: Raised when the user does not have permission to access the KGs.
+            RequestFailureException: Raised when the request fails due to an unexpected error.
+
+        Example:
+            >>> kg = PollyKG()
+            >>> # Get only published KGs
+            >>> kgs = kg.get_all_kgs()
+            >>> for kg_info in kgs:
+            ...     print(f"{kg_info['kg_name']} (ID: {kg_info['kg_id']})")
+            base kg v3 (ID: 14_base_kg_v3)
+
+            >>> # Get all KGs including unpublished ones with instance details
+            >>> kgs_with_instances = kg.get_all_kgs(
+            ...     include_unpublished=True,
+            ...     include_instances=True,
+            ...     include_terminated=True
+            ... )
+            >>> for kg_info in kgs_with_instances:
+            ...     print(f"{kg_info['kg_name']} - {len(kg_info.get('instances', []))} instances")
+        """
+        try:
+            kg_url = f"{self.polly_kg_neo4j_endpoint}/kg"
+
+            # Build query parameters
+            params = {}
+            if include_unpublished:
+                params["include_unpublished"] = "true"
+            if include_instances:
+                params["include_instances"] = "true"
+            if include_terminated:
+                params["include_terminated"] = "true"
+
+            response = self.session.get(kg_url, params=params)
+            handle_success_and_error_response(response)
+
+            data = response.json().get("data", [])
+
+            if not data:
+                raise ResourceNotFoundError(detail="No knowledge graphs found.")
+
+            return data
+
+        except Exception as e:
+            print(e)
+            raise

{polly_python-4.2.0 → polly_python-4.4.0}/polly/s3_utils.py

@@ -596,7 +596,7 @@ def _copy_remote_file(
             part_id = i + 1
             part = ctx.s3_client.upload_part_copy(
                 CopySource=src_params,
-                CopySourceRange=f"bytes={start}-{end-1}",
+                CopySourceRange=f"bytes={start}-{end - 1}",
                 Bucket=dest_bucket,
                 Key=dest_key,
                 UploadId=upload_id,

{polly_python-4.2.0 → polly_python-4.4.0/polly_python.egg-info}/PKG-INFO

@@ -1,36 +1,47 @@
 Metadata-Version: 2.4
 Name: polly_python
-Version: 4.2.0
+Version: 4.4.0
 Summary: Polly SDK
 Home-page: https://github.com/ElucidataInc/polly-python
 Project-URL: Documentation, https://docs.elucidata.io
 Project-URL: Tutorial Notebooks, https://github.com/ElucidataInc/polly-python
-Requires-Python: <3.12,>=3.9
+Requires-Python: <3.15,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
-Requires-Dist: cmapPy<=4.0.1
-Requires-Dist: cloudpathlib>=0.15.0
+Requires-Dist: cmapPy==4.0.1
+Requires-Dist: cloudpathlib<1.0.0,>=0.19.0
 Requires-Dist: retrying==1.3.4
 Requires-Dist: rst2txt==1.1.0
-Requires-Dist: python-jose==3.3.0
-Requires-Dist: mixpanel==4.10.0
-Requires-Dist: Deprecated>=1.2.12
-Requires-Dist: pytest>=6.2.5
-Requires-Dist: cryptography<=38.0.0,>=37.0.1
-Requires-Dist: plotly>=5.0.0; python_version >= "3.7"
-Requires-Dist: pandas<=2.2.2,>=1.3.5; python_version >= "3.7"
-Requires-Dist: numpy<=1.26.4
-Requires-Dist: pydantic==1.10.12; python_version >= "3.7"
-Requires-Dist: requests==2.28.1
-Requires-Dist: boto3<2.0,>=1.24.0; python_version >= "3.7"
-Requires-Dist: botocore<2.0,>=1.27.0; python_version >= "3.7"
-Requires-Dist: joblib>=1.2.0; python_version >= "3.7"
-Requires-Dist: tabulate==0.9.0
-Requires-Dist: tqdm==4.65.0; python_version >= "3.7"
+Requires-Dist: mixpanel<5.0.0,>=4.10.0
+Requires-Dist: Deprecated<2.0.0,>=1.2.12
+Requires-Dist: pydantic<3.0.0,>=2.8.2
+Requires-Dist: requests<=2.32.3,>=2.31.0
+Requires-Dist: boto3<2.0.0,>=1.34.0
+Requires-Dist: joblib==1.4.2
+Requires-Dist: rich<14.0.0,>=13.0.0
+Requires-Dist: tqdm==4.66.4
+Requires-Dist: plotly==6.3.1
+Requires-Dist: cryptography<=38.0.0; python_full_version >= "3.9.0" and python_full_version <= "3.9.1"
+Requires-Dist: cryptography==46.0.2; python_full_version >= "3.9.2"
+Requires-Dist: setuptools>=65.0.0; python_version >= "3.12"
+Requires-Dist: pandas<=2.2.3,>=1.5.3; python_version == "3.9"
+Requires-Dist: pandas<=2.2.3,>=1.5.3; python_version == "3.10"
+Requires-Dist: pandas<=2.2.3,>=1.5.3; python_version == "3.11"
+Requires-Dist: pandas<=2.2.3,>=2.1.0; python_version == "3.12"
+Requires-Dist: pandas<=2.2.3,>=2.2.2; python_version == "3.13"
+Requires-Dist: pandas<=2.2.3,>=2.2.2; python_version == "3.14"
+Requires-Dist: numpy<=1.25.2,>=1.23.0; python_version == "3.9"
+Requires-Dist: numpy<=2.2.2,>=1.23.0; python_version == "3.10"
+Requires-Dist: numpy<=2.2.2,>=1.24.0; python_version == "3.11"
+Requires-Dist: numpy<=2.2.2,>=1.26.0; python_version == "3.12"
+Requires-Dist: numpy<=2.2.2,>=2.2.0; python_version == "3.13"
+Requires-Dist: numpy<=2.2.2,>=2.2.0; python_version == "3.14"
 Provides-Extra: testing
 Requires-Dist: black; extra == "testing"
 Requires-Dist: flake8; extra == "testing"
 Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-mock; extra == "testing"
+Requires-Dist: moto; extra == "testing"
 Dynamic: license-file
 
 [![made-with-python](https://img.shields.io/badge/Made%20with-Python-1f425f.svg)](https://www.python.org/)

polly_python-4.4.0/polly_python.egg-info/requires.txt

@@ -0,0 +1,53 @@
+cmapPy==4.0.1
+cloudpathlib<1.0.0,>=0.19.0
+retrying==1.3.4
+rst2txt==1.1.0
+mixpanel<5.0.0,>=4.10.0
+Deprecated<2.0.0,>=1.2.12
+pydantic<3.0.0,>=2.8.2
+requests<=2.32.3,>=2.31.0
+boto3<2.0.0,>=1.34.0
+joblib==1.4.2
+rich<14.0.0,>=13.0.0
+tqdm==4.66.4
+plotly==6.3.1
+
+[:python_full_version >= "3.9.0" and python_full_version <= "3.9.1"]
+cryptography<=38.0.0
+
+[:python_full_version >= "3.9.2"]
+cryptography==46.0.2
+
+[:python_version == "3.10"]
+pandas<=2.2.3,>=1.5.3
+numpy<=2.2.2,>=1.23.0
+
+[:python_version == "3.11"]
+pandas<=2.2.3,>=1.5.3
+numpy<=2.2.2,>=1.24.0
+
+[:python_version == "3.12"]
+pandas<=2.2.3,>=2.1.0
+numpy<=2.2.2,>=1.26.0
+
+[:python_version == "3.13"]
+pandas<=2.2.3,>=2.2.2
+numpy<=2.2.2,>=2.2.0
+
+[:python_version == "3.14"]
+pandas<=2.2.3,>=2.2.2
+numpy<=2.2.2,>=2.2.0
+
+[:python_version == "3.9"]
+pandas<=2.2.3,>=1.5.3
+numpy<=1.25.2,>=1.23.0
+
+[:python_version >= "3.12"]
+setuptools>=65.0.0
+
+[testing]
+black
+flake8
+pytest
+pytest-mock
+moto

{polly_python-4.2.0 → polly_python-4.4.0}/polly_services/dataset.py

@@ -120,9 +120,9 @@ class S3ClientManager:
     def _init_client(self) -> S3SessionDetails:
         if (self.omixatlas_id, self.copy_dest_omixatlas_id) not in self._cache:
             session_details = self._get_autorefresh_session()
-            self._cache[
-                (self.omixatlas_id, self.copy_dest_omixatlas_id)
-            ] = session_details
+            self._cache[(self.omixatlas_id, self.copy_dest_omixatlas_id)] = (
+                session_details
+            )
 
         return self._cache[(self.omixatlas_id, self.copy_dest_omixatlas_id)]
 

{polly_python-4.2.0 → polly_python-4.4.0}/polly_services/files/files_hlpr.py

@@ -3,7 +3,6 @@ from polly import helpers
 from polly_services import polly_services_hlpr
 import json
 from polly import constants as const
-from tabulate import tabulate
 from functools import lru_cache
 import pandas as pd
 import copy
@@ -1217,9 +1216,9 @@ def upload_metadata_to_s3(
                 combined_metadata_file_path,
                 metadata_upload_details["metadata_directory"],
             )
-            file_status_dict[
-                const.COMBINED_METADATA_FILE_NAME
-            ] = const.UPLOAD_URL_CREATED
+            file_status_dict[const.COMBINED_METADATA_FILE_NAME] = (
+                const.UPLOAD_URL_CREATED
+            )
         except Exception as err:
             if isinstance(err, S3UploadFailedError) and const.EXPIRED_TOKEN in str(err):
                 (
@@ -1241,13 +1240,13 @@ def upload_metadata_to_s3(
                     combined_metadata_file_path,
                     metadata_upload_details["metadata_directory"],
                 )
-                file_status_dict[
-                    const.COMBINED_METADATA_FILE_NAME
-                ] = const.UPLOAD_URL_CREATED
+                file_status_dict[const.COMBINED_METADATA_FILE_NAME] = (
+                    const.UPLOAD_URL_CREATED
+                )
             else:
-                file_status_dict[
-                    const.COMBINED_METADATA_FILE_NAME
-                ] = const.UPLOAD_ERROR_CODE
+                file_status_dict[const.COMBINED_METADATA_FILE_NAME] = (
+                    const.UPLOAD_ERROR_CODE
+                )
                 raise err
     return file_status_dict
 
@@ -2673,11 +2672,4 @@ def convert_delete_datasets_res_dict_to_df(result_dict: dict):
             df_list.append(df_1)
 
     data_delete_df = pd.concat(df_list, axis=0, ignore_index=True)
-    print(
-        tabulate(
-            data_delete_df,
-            headers="keys",
-            tablefmt="fancy_grid",
-            maxcolwidths=[None, 10, None],
-        )
-    )
+    print(data_delete_df.to_string(index=False, max_colwidth=10))

{polly_python-4.2.0 → polly_python-4.4.0}/polly_services/schema/schema.py

@@ -2,7 +2,6 @@ from polly_interfaces.ISchema import ISchema
 from polly.errors import error_handler
 from polly import constants as const
 import json
-from tabulate import tabulate
 from polly import helpers
 from polly_services import polly_services_hlpr
 from polly_services.schema import schema_hlpr
@@ -148,13 +147,11 @@ class Schema(ISchema):
                 print("Schema has no errors")
             else:
                 print(
-                    "Schema insert/update/replace/validate didn’t go through because there are errors in "
+                    "Schema insert/update/replace/validate didn't go through because there are errors in "
                     + "the schema. Those errors is summarised in the table below: "
                 )
                 print("\n")
-                print(
-                    tabulate(error_res_combined, headers="keys", tablefmt="fancy_grid")
-                )
+                print(error_res_combined.to_string(index=False))
             return error_res_combined
 
         except Exception as err:

{polly_python-4.2.0 → polly_python-4.4.0}/polly_services/schema/validate_schema_hlpr.py

@@ -1,4 +1,12 @@
-from pydantic import BaseModel, constr, create_model, validator, ValidationError, conint
+from pydantic import (
+    BaseModel,
+    constr,
+    create_model,
+    field_validator,
+    ValidationError,
+    conint,
+    ValidationInfo,
+)
 from typing import Optional
 import pandas as pd
 import copy
@@ -21,19 +29,21 @@ class FieldType(str, Enum):
 class AttributeModel(BaseModel):
     original_name: constr(strict=True, min_length=1, max_length=50)
     type: FieldType
-    is_keyword: Optional[bool]
-    is_array: Optional[bool]
-    is_column: Optional[bool]
-    is_curated: Optional[bool]
-    is_searchable: Optional[bool]
+    is_keyword: Optional[bool] = None
+    is_array: Optional[bool] = None
+    is_column: Optional[bool] = None
+    is_curated: Optional[bool] = None
+    is_searchable: Optional[bool] = None
     filter_size: conint(ge=1, le=3000) = 500
     display_name: constr(strict=True, min_length=1, max_length=50)
     description: constr(strict=True, min_length=1, max_length=300)
-    is_ontology: Optional[bool]
-    is_filter: Optional[bool]
+    is_ontology: Optional[bool] = None
+    is_filter: Optional[bool] = None
 
-    @validator("is_filter")
-    def is_filter_check(cls, is_filter, values):
+    @field_validator("is_filter")
+    @classmethod
+    def is_filter_check(cls, is_filter, info: ValidationInfo):
+        values = info.data
         if is_filter:
             if not values.get("is_keyword"):
                 raise ValueError(
@@ -110,10 +120,15 @@ def _validate_schema_values(field_dict: dict):
     Create pydantic model to validate schema values
     """
     field_name = field_dict["field_name"]
+
+    # Create a field_validator for the field_name in V2 style
+    def check_field_name_wrapper(cls, value):
+        return _check_field_name(cls, value)
+
     validators = {
-        "check_field_name": validator(
-            "field_name", allow_reuse=True, check_fields=False
-        )(_check_field_name)
+        "check_field_name": field_validator("field_name")(
+            classmethod(check_field_name_wrapper)
+        )
     }
     schema_model = _build_schema_validation_model(field_name, validators)
     try:

polly_python-4.4.0/setup.cfg

@@ -0,0 +1,78 @@
+[metadata]
+description_file = README.md
+name = polly_python
+version = attr: polly.__version__
+description = Polly SDK
+url = https://github.com/ElucidataInc/polly-python
+long_description = file: README.md
+long_description_content_type = text/markdown
+project_urls = 
+	Documentation = https://docs.elucidata.io
+	Tutorial Notebooks = https://github.com/ElucidataInc/polly-python
+
+[options]
+packages = find:
+setup_requires = wheel
+python_requires = >=3.9, <3.15
+install_requires = 
+	cmapPy == 4.0.1
+	cloudpathlib >= 0.19.0, < 1.0.0
+	retrying == 1.3.4
+	rst2txt == 1.1.0
+	mixpanel >= 4.10.0, < 5.0.0
+	Deprecated >= 1.2.12, < 2.0.0
+	pydantic >= 2.8.2, < 3.0.0
+	requests >= 2.31.0, <= 2.32.3
+	boto3 >= 1.34.0, < 2.0.0
+	joblib == 1.4.2
+	rich >= 13.0.0, < 14.0.0
+	tqdm == 4.66.4
+	plotly == 6.3.1
+	cryptography <= 38.0.0 ; python_full_version >= '3.9.0' and python_full_version <= '3.9.1'
+	cryptography == 46.0.2 ; python_full_version >= '3.9.2'
+	setuptools >= 65.0.0 ; python_version >= '3.12'
+	
+	pandas >= 1.5.3, <= 2.2.3 ; python_version == '3.9'
+	pandas >= 1.5.3, <= 2.2.3 ; python_version == '3.10'
+	pandas >= 1.5.3, <= 2.2.3 ; python_version == '3.11'
+	pandas >= 2.1.0, <= 2.2.3 ; python_version == '3.12'
+	pandas >= 2.2.2, <= 2.2.3 ; python_version == '3.13'
+	pandas >= 2.2.2, <= 2.2.3 ; python_version == '3.14'
+	
+	numpy >= 1.23.0, <= 1.25.2 ; python_version == '3.9'
+	numpy >= 1.23.0, <= 2.2.2 ; python_version == '3.10'
+	numpy >= 1.24.0, <= 2.2.2 ; python_version == '3.11'
+	numpy >= 1.26.0, <= 2.2.2 ; python_version == '3.12'
+	numpy >= 2.2.0, <= 2.2.2 ; python_version == '3.13'
+	numpy >= 2.2.0, <= 2.2.2 ; python_version == '3.14'
+include_package_data = True
+
+[options.packages.find]
+exclude = 
+	tests*
+	build*
+	dist*
+	docs*
+	consumption_pipelines*
+
+[options.extras_require]
+testing = 
+	black
+	flake8
+	pytest
+	pytest-mock
+	moto
+
+[flake8]
+exclude = build,.git, docs, dist, consumption_pipelines
+extend-ignore = E731,W503
+max-line-length = 127
+max-complexity = 10
+
+[black]
+exclude = build,.git, docs, dist, consumption_pipelines
+
+[egg_info]
+tag_build = 
+tag_date = 0
+

{polly_python-4.2.0 → polly_python-4.4.0}/tests/test_kg.py

@@ -222,3 +222,124 @@ def test_get_schema_success(mocker):
     result = obj.get_schema()
 
     assert "Disease" in result["schema"]["labels"]
+
+
+def test_get_all_kgs_success(mocker):
+    mocker.patch("polly.polly_kg._get_default_kg", return_value=("kg1", "v1"))
+
+    obj = PollyKG(token=token)
+    mock_response = mocker.Mock()
+    mock_response.status_code = 200
+    mock_response.json.return_value = {
+        "data": [
+            {
+                "kg_id": "14_base_kg_v3",
+                "kg_name": "base kg v3",
+                "kg_description": "Base KG v",
+                "version_id": 1,
+                "created_at": 1756115807076,
+                "published": True,
+            },
+            {
+                "kg_id": "15_test_kg",
+                "kg_name": "test kg",
+                "kg_description": "Test KG",
+                "version_id": 2,
+                "created_at": 1756115900000,
+                "published": False,
+            },
+        ]
+    }
+
+    mocker.patch.object(obj.session, "get", return_value=mock_response)
+    result = obj.get_all_kgs()
+
+    assert isinstance(result, list)
+    assert len(result) == 2
+    assert result[0]["kg_id"] == "14_base_kg_v3"
+    assert result[0]["kg_name"] == "base kg v3"
+    assert result[0]["version_id"] == 1
+    assert result[0]["published"] is True
+    assert result[1]["kg_id"] == "15_test_kg"
+    assert result[1]["published"] is False
+
+
+def test_get_all_kgs_with_parameters(mocker):
+    mocker.patch("polly.polly_kg._get_default_kg", return_value=("kg1", "v1"))
+
+    obj = PollyKG(token=token)
+    mock_response = mocker.Mock()
+    mock_response.status_code = 200
+    mock_response.json.return_value = {
+        "data": [
+            {
+                "kg_id": "14_base_kg_v3",
+                "kg_name": "base kg v3",
+                "kg_description": "Base KG v",
+                "version_id": 1,
+                "created_at": 1756115807076,
+                "published": True,
+                "instances": [
+                    {
+                        "instance_id": "inst_123",
+                        "instance_type": "t3.medium",
+                        "is_terminated": False,
+                        "default_instance": True,
+                        "org_id": 1,
+                        "created_at": 1756115807076,
+                    }
+                ],
+            },
+            {
+                "kg_id": "15_test_kg",
+                "kg_name": "test kg",
+                "kg_description": "Test KG",
+                "version_id": 2,
+                "created_at": 1756115900000,
+                "published": False,
+                "instances": [
+                    {
+                        "instance_id": "inst_456",
+                        "instance_type": "t3.large",
+                        "is_terminated": True,
+                        "default_instance": False,
+                        "org_id": 1,
+                        "created_at": 1756115900000,
+                    }
+                ],
+            },
+        ]
+    }
+
+    mock_get = mocker.patch.object(obj.session, "get", return_value=mock_response)
+    result = obj.get_all_kgs(
+        include_unpublished=True, include_instances=True, include_terminated=True
+    )
+
+    # Verify the API was called with correct parameters
+    mock_get.assert_called_once()
+    call_kwargs = mock_get.call_args.kwargs
+    assert "params" in call_kwargs
+    assert call_kwargs["params"] == {
+        "include_unpublished": "true",
+        "include_instances": "true",
+        "include_terminated": "true",
+    }
+
+    # Verify the response structure
+    assert isinstance(result, list)
+    assert len(result) == 2
+    assert result[0]["kg_id"] == "14_base_kg_v3"
+    assert result[0]["published"] is True
+    assert "instances" in result[0]
+    assert len(result[0]["instances"]) == 1
+    assert result[0]["instances"][0]["instance_id"] == "inst_123"
+    assert result[0]["instances"][0]["instance_type"] == "t3.medium"
+    assert result[0]["instances"][0]["is_terminated"] is False
+
+    assert result[1]["kg_id"] == "15_test_kg"
+    assert result[1]["published"] is False
+    assert "instances" in result[1]
+    assert len(result[1]["instances"]) == 1
+    assert result[1]["instances"][0]["instance_id"] == "inst_456"
+    assert result[1]["instances"][0]["is_terminated"] is True

{polly_python-4.2.0 → polly_python-4.4.0}/tests/test_omixatlas.py

@@ -1018,7 +1018,7 @@ def test_validate_schema_function_field_name_having_original_name_empty(
     msg_val = res_df.iloc[0]["message"]
 
     assert isinstance(res_df, pd.DataFrame)
-    assert "ensure this value has at least 1 characters" in msg_val
+    assert "String should have at least 1 character" in msg_val
 
 
 def test_validate_schema_function_field_name_having_original_name_greater_than_50_chars(
@@ -1039,7 +1039,7 @@ def test_validate_schema_function_field_name_having_original_name_greater_than_5
     msg_val = res_df.iloc[0]["message"]
 
     assert isinstance(res_df, pd.DataFrame)
-    assert "ensure this value has at most 50 characters" in msg_val
+    assert "String should have at most 50 characters" in msg_val
 
 
 def test_validate_schema_function_field_name_having_type_is_not_supported(
@@ -1061,8 +1061,7 @@ def test_validate_schema_function_field_name_having_type_is_not_supported(
 
     assert isinstance(res_df, pd.DataFrame)
     assert (
-        "value is not a valid enumeration member; permitted: 'boolean', 'integer', 'float', 'text', 'object'"
-        in msg_val
+        "Input should be 'boolean', 'integer', 'float', 'text' or 'object'" in msg_val
     )
 
 
@@ -1084,7 +1083,7 @@ def test_validate_schema_function_field_name_having_is_array_string(
     msg_val = res_df.iloc[0]["message"]
 
     assert isinstance(res_df, pd.DataFrame)
-    assert "value could not be parsed to a boolean" in msg_val
+    assert "Input should be a valid boolean" in msg_val
 
 
 def test_validate_schema_function_field_name_having_is_keyword_string(
@@ -1104,7 +1103,7 @@ def test_validate_schema_function_field_name_having_is_keyword_string(
     res_df = omix_obj.validate_schema(test_data)
     msg_val = res_df.iloc[0]["message"]
     assert isinstance(res_df, pd.DataFrame)
-    assert "value could not be parsed to a boolean" in msg_val
+    assert "Input should be a valid boolean" in msg_val
 
 
 def test_validate_schema_function_field_name_having_filter_size_less(
@@ -1125,7 +1124,7 @@ def test_validate_schema_function_field_name_having_filter_size_less(
     res_df = omix_obj.validate_schema(test_data)
     msg_val = res_df.iloc[0]["message"]
     assert isinstance(res_df, pd.DataFrame)
-    assert "ensure this value is greater than or equal to 1" in msg_val
+    assert "Input should be greater than or equal to 1" in msg_val
 
 
 def test_validate_schema_function_field_name_having_filter_size_greater(
@@ -1145,7 +1144,7 @@ def test_validate_schema_function_field_name_having_filter_size_greater(
     res_df = omix_obj.validate_schema(test_data)
     msg_val = res_df.iloc[0]["message"]
     assert isinstance(res_df, pd.DataFrame)
-    assert "ensure this value is less than or equal to 3000" in msg_val
+    assert "Input should be less than or equal to 3000" in msg_val
 
 
 def test_validate_schema_function_field_name_having_display_name_empty(
@@ -1167,7 +1166,7 @@ def test_validate_schema_function_field_name_having_display_name_empty(
     msg_val = res_df.iloc[0]["message"]
     assert isinstance(res_df, pd.DataFrame)
     assert "display_name" in loc
-    assert "ensure this value has at least 1 characters" in msg_val
+    assert "String should have at least 1 character" in msg_val
 
 
 def test_validate_schema_function_field_name_having_display_name_greater(
@@ -1190,7 +1189,7 @@ def test_validate_schema_function_field_name_having_display_name_greater(
     msg_val = res_df.iloc[0]["message"]
     assert isinstance(res_df, pd.DataFrame)
     assert "display_name" in loc
-    assert "ensure this value has at most 50 characters" in msg_val
+    assert "String should have at most 50 characters" in msg_val
 
 
 def test_validate_schema_function_field_name_having_is_filter_is_keyword(
@@ -1272,7 +1271,7 @@ def test_validate_schema_function_having_original_name_int(
     attribute_val = res_df.iloc[0]["attribute"]
     assert isinstance(res_df, pd.DataFrame)
     assert attribute_val == "original_name"
-    assert "str type expected" in msg_val
+    assert "Input should be a valid string" in msg_val
 
 
 def test_validate_schema_function_having_field_size_str(
@@ -1294,7 +1293,7 @@ def test_validate_schema_function_having_field_size_str(
     attribute_val = res_df.iloc[0]["attribute"]
     assert isinstance(res_df, pd.DataFrame)
     assert attribute_val == "filter_size"
-    assert "value is not a valid integer" in msg_val
+    assert "Input should be a valid integer" in msg_val
 
 
 # def test_download_metadata():
@@ -2545,21 +2544,9 @@ def validate_schema_mock_fixture(
     get_omixatlas_mock_fixture_polly_services,
     get_ingestion_test_1_schema_fixture,
 ):
-    # mocker.patch(
-    #     polly.omixatlas.__name__ + ".OmixAtlas._get_omixatlas",
-    #     return_value=get_omixatlas_mock_fixture,
-    # )
-
-    mocker.patch(
-        polly_services.polly_services_hlpr.__name__ + ".get_omixatlas",
-        return_value=get_omixatlas_mock_fixture_polly_services,
-    )
-
-    Polly.auth(testpolly_token, env="testpolly")
-    omix_obj = omixatlas.OmixAtlas()
-
-    body = get_ingestion_test_1_schema_fixture
-    error_df = omix_obj.validate_schema(body)
+    # Return an empty DataFrame (no validation errors) for positive test cases
+    # This fixture is used to mock validate_schema to skip actual validation
+    error_df = pd.DataFrame()
     return error_df
 
 

{polly_python-4.2.0 → polly_python-4.4.0}/tests/test_s3_utils.py

@@ -1,6 +1,6 @@
 import pytest
 import boto3
-from moto import mock_s3
+from moto import mock_aws
 from polly.s3_utils import copy_file
 
 
@@ -16,7 +16,7 @@ def aws_credentials():
 
 @pytest.fixture
 def s3_client(aws_credentials):
-    with mock_s3():
+    with mock_aws():
         conn = boto3.client("s3", region_name="us-east-1")
         yield conn
 

polly_python-4.2.0/polly/__init__.py

@@ -1 +0,0 @@
-__version__ = "4.2.0"

polly_python-4.2.0/polly_python.egg-info/requires.txt

@@ -1,26 +0,0 @@
-cmapPy<=4.0.1
-cloudpathlib>=0.15.0
-retrying==1.3.4
-rst2txt==1.1.0
-python-jose==3.3.0
-mixpanel==4.10.0
-Deprecated>=1.2.12
-pytest>=6.2.5
-cryptography<=38.0.0,>=37.0.1
-numpy<=1.26.4
-requests==2.28.1
-tabulate==0.9.0
-
-[:python_version >= "3.7"]
-plotly>=5.0.0
-pandas<=2.2.2,>=1.3.5
-pydantic==1.10.12
-boto3<2.0,>=1.24.0
-botocore<2.0,>=1.27.0
-joblib>=1.2.0
-tqdm==4.65.0
-
-[testing]
-black
-flake8
-pytest

polly_python-4.2.0/setup.cfg

@@ -1,65 +0,0 @@
-[metadata]
-description_file = README.md
-name = polly_python
-version = attr: polly.__version__
-description = Polly SDK
-url = https://github.com/ElucidataInc/polly-python
-long_description = file: README.md
-long_description_content_type = text/markdown
-project_urls = 
-	Documentation = https://docs.elucidata.io
-	Tutorial Notebooks = https://github.com/ElucidataInc/polly-python
-
-[options]
-packages = find:
-setup_requires = wheel
-python_requires = >=3.9, <3.12
-install_requires = 
-	cmapPy <= 4.0.1
-	cloudpathlib >= 0.15.0
-	retrying == 1.3.4
-	rst2txt == 1.1.0
-	python-jose == 3.3.0
-	mixpanel == 4.10.0
-	Deprecated >= 1.2.12
-	pytest >= 6.2.5
-	cryptography >= 37.0.1, <= 38.0.0
-	plotly >= 5.0.0 ; python_version >= '3.7'
-	pandas >= 1.3.5, <= 2.2.2 ; python_version >= '3.7'
-	numpy <= 1.26.4
-	pydantic == 1.10.12 ; python_version >= '3.7'
-	requests == 2.28.1
-	boto3 >= 1.24.0, <2.0; python_version >= '3.7'
-	botocore >= 1.27.0, <2.0; python_version >= '3.7'
-	joblib >= 1.2.0 ; python_version >= '3.7'
-	tabulate == 0.9.0
-	tqdm == 4.65.0 ; python_version >= '3.7'
-include_package_data = True
-
-[options.packages.find]
-exclude = 
-	tests*
-	build*
-	dist*
-	docs*
-	consumption_pipelines*
-
-[options.extras_require]
-testing = 
-	black
-	flake8
-	pytest
-
-[flake8]
-exclude = build,.git, docs, dist, consumption_pipelines
-extend-ignore = E731,W503
-max-line-length = 127
-max-complexity = 10
-
-[black]
-exclude = build,.git, docs, dist, consumption_pipelines
-
-[egg_info]
-tag_build = 
-tag_date = 0
-