willisapi-client 1.8__tar.gz → 1.9.1__tar.gz

{willisapi_client-1.8 → willisapi_client-1.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: willisapi_client
-Version: 1.8
+Version: 1.9.1
 Summary: A Python client for willisapi
 Home-page: https://github.com/bklynhlth/willsiapi_client
 Author: bklynhlth
@@ -39,7 +39,7 @@ Conversion notes:
 
 WillisAPI Client is the python interface for Brooklyn Health’s WillisAPI.
 
-Official documentation for WillisAPI Client can be found in the [Github Wiki](www.github.com/bklynhlth/willisapi_client/wiki).
+Official documentation for WillisAPI Client can be found in the [Github Wiki](http://www.github.com/bklynhlth/willisapi_client/wiki).
 
 To learn more about Brooklyn Health or WillisAPI, visit [brooklyn.health](https://www.brooklyn.health) or [getintouch@brooklyn.health](mailto:getintouch@brooklyn.health).
 
@@ -82,10 +82,10 @@ measures = willisapi.download(key, 'project_name')
 ```
 
 
-If you run into trouble while using the client, please raise it in the [Issues](www.github.com/bklynhlth/willisapi_client/issues) tab. 
+If you run into trouble while using the client, please raise it in the [Issues](http://www.github.com/bklynhlth/willisapi_client/issues) tab. 
 
 ***
 
 Brooklyn Health is a small team of clinicians, scientists, and engineers based in Brooklyn, NY. 
 
-We develop and maintain [OpenWillis](www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 
+We develop and maintain [OpenWillis](http://www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 

{willisapi_client-1.8 → willisapi_client-1.9.1}/README.md

@@ -27,7 +27,7 @@ Conversion notes:
 
 WillisAPI Client is the python interface for Brooklyn Health’s WillisAPI.
 
-Official documentation for WillisAPI Client can be found in the [Github Wiki](www.github.com/bklynhlth/willisapi_client/wiki).
+Official documentation for WillisAPI Client can be found in the [Github Wiki](http://www.github.com/bklynhlth/willisapi_client/wiki).
 
 To learn more about Brooklyn Health or WillisAPI, visit [brooklyn.health](https://www.brooklyn.health) or [getintouch@brooklyn.health](mailto:getintouch@brooklyn.health).
 
@@ -70,10 +70,10 @@ measures = willisapi.download(key, 'project_name')
 ```
 
 
-If you run into trouble while using the client, please raise it in the [Issues](www.github.com/bklynhlth/willisapi_client/issues) tab. 
+If you run into trouble while using the client, please raise it in the [Issues](http://www.github.com/bklynhlth/willisapi_client/issues) tab. 
 
 ***
 
 Brooklyn Health is a small team of clinicians, scientists, and engineers based in Brooklyn, NY. 
 
-We develop and maintain [OpenWillis](www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 
+We develop and maintain [OpenWillis](http://www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 

willisapi_client-1.9.1/tests/test_diarize.py

@@ -0,0 +1,64 @@
+from unittest.mock import patch
+
+from willisapi_client.services.diarize.willisdiarize import (
+    willis_diarize,
+)
+from willisapi_client.logging_setup import logger as logger
+import logging
+
+
+class TestDiarizeFunction:
+    def setup(self):
+        self.key = "dummy"
+        self.file_path = "file.json"
+
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.decode_response"
+    )
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.request_diarize"
+    )
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.read_json_file"
+    )
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.is_valid_file_path"
+    )
+    def test_willis_diarize_function_success(
+        self, mock_file_path, mock_json, mock_api_res, mock_decoded_res, caplog
+    ):
+        mock_file_path.return_value = True
+        mock_json.return_value = {"Correct Transcription"}
+        mock_api_res.return_value = {
+            "status_code": 200,
+            "data": "Encoded Response",
+        }
+        mock_decoded_res.return_value = {"Correct Transcription"}
+        with caplog.at_level(logging.INFO):
+            res = willis_diarize(self.key, self.file_path)
+
+        assert res == {"Correct Transcription"}
+
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.request_diarize"
+    )
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.read_json_file"
+    )
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.is_valid_file_path"
+    )
+    def test_willis_diarize_function_invalid_json(
+        self, mock_file_path, mock_json, mock_api_res, caplog
+    ):
+        mock_file_path.return_value = False
+        mock_json.return_value = {}
+        mock_api_res.return_value = {
+            "status_code": 200,
+            "data": "Encoded Response",
+        }
+
+        with caplog.at_level(logging.INFO):
+            res = willis_diarize(self.key, self.file_path)
+
+        assert "Input file type is incorrect. We only accept JSON files" in caplog.text

willisapi_client-1.9.1/tests/test_diarize_call_remaining.py

@@ -0,0 +1,42 @@
+from unittest.mock import patch
+
+from willisapi_client.services.diarize.willisdiarize_call_remaining import (
+    willis_diarize_call_remaining,
+)
+from willisapi_client.logging_setup import logger as logger
+import logging
+
+
+class TestDiarizeCallsFunction:
+    def setup(self):
+        self.key = "dummy"
+
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.request_call_remaining"
+    )
+    def test_willisdiarize_remaining_calls_failed(self, mocked_data, caplog):
+        mocked_data.return_value = {}
+        with caplog.at_level(logging.INFO):
+            willis_diarize_call_remaining(self.key)
+        assert "" in caplog.text
+
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.request_call_remaining"
+    )
+    def test_willisdiarize_remaining_calls_missing_auth(self, mocked_data, caplog):
+        mocked_data.return_value = {"status_code": 401, "message": "message"}
+        with caplog.at_level(logging.INFO):
+            willis_diarize_call_remaining(self.key)
+        assert "message" in caplog.text
+
+    @patch(
+        "willisapi_client.services.diarize.diarize_utils.DiarizeUtils.request_call_remaining"
+    )
+    def test_willisdiarize_remaining_calls_success(self, mocked_data, caplog):
+        mocked_data.return_value = {
+            "status_code": 401,
+            "message": "Your account has 10 WillisDiarize API calls remaining.",
+        }
+        with caplog.at_level(logging.INFO):
+            willis_diarize_call_remaining(self.key)
+        assert "Your account has 10 WillisDiarize API calls remaining." in caplog.text

willisapi_client-1.9.1/willisapi_client/__init__.py

@@ -0,0 +1,18 @@
+# website:   https://www.brooklyn.health
+
+# import the required packages
+from willisapi_client.services.api import (
+    login,
+    upload,
+    download,
+    willis_diarize_call_remaining,
+    willis_diarize,
+)
+
+__all__ = [
+    "login",
+    "upload",
+    "download",
+    "willis_diarize_call_remaining",
+    "willis_diarize",
+]

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client/__version__.py

@@ -1,7 +1,8 @@
 """Version details for willisapi_client
 """
+
 __client__ = "willisapi_client"
-__latestVersion__ = "1.8"
+__latestVersion__ = "1.9.1"
 __url__ = "https://github.com/bklynhlth/willsiapi_client"
 __short_description__ = "A Python client for willisapi"
 __content_type__ = "text/markdown"

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client/services/api.py

@@ -4,3 +4,7 @@
 from willisapi_client.services.auth import login
 from willisapi_client.services.upload import upload
 from willisapi_client.services.download import download
+from willisapi_client.services.diarize import (
+    willis_diarize_call_remaining,
+    willis_diarize,
+)

willisapi_client-1.9.1/willisapi_client/services/diarize/__init__.py

@@ -0,0 +1,7 @@
+# website:   https://www.brooklyn.health
+from willisapi_client.services.diarize.willisdiarize_call_remaining import (
+    willis_diarize_call_remaining,
+)
+from willisapi_client.services.diarize.willisdiarize import willis_diarize
+
+__all__ = ["willis_diarize_call_remaining", "willis_diarize"]

willisapi_client-1.9.1/willisapi_client/services/diarize/diarize_utils.py

@@ -0,0 +1,99 @@
+import requests
+import json
+import time
+import random
+import os
+import gzip
+import base64
+from willisapi_client.logging_setup import logger as logger
+
+
+class DiarizeUtils:
+    def is_valid_file_path(file_path: str):
+        return file_path.endswith(".json") and os.path.exists(file_path)
+
+    def read_json_file(file_path: str):
+        data = None
+        try:
+            with open(file_path) as f:
+                json_data = json.load(f)
+            data = dict(json_data=json_data)
+        except json.decoder.JSONDecodeError:
+            logger.info("No data found in the file or JSON is invalid.")
+            logger.info("Failed!")
+        return data
+
+    def decode_response(encoded_response):
+        return json.loads(gzip.decompress(base64.b64decode(encoded_response)))
+
+    def request_diarize(url, data, headers, try_number):
+        """
+        ------------------------------------------------------------------------------------------------------
+        Class: DiarizeUtils
+
+        Function: request_diarize
+
+        Description: This is an internal diarize function which makes a GET API call to brooklyn.health API server
+
+        Parameters:
+        ----------
+        url: The URL of the API endpoint.
+        headers: The headers to be sent in the request.
+        try_number: The number of times the function has been tried.
+
+        Returns:
+        ----------
+        json: The JSON response from the API server.
+        ------------------------------------------------------------------------------------------------------
+        """
+        try:
+            response = requests.post(url, json=data, headers=headers)
+            res_json = response.json()
+        except (
+            requests.exceptions.ConnectionError,
+            json.decoder.JSONDecodeError,
+        ) as ex:
+            if try_number == 3:
+                raise
+            time.sleep(random.random() * 2)
+            return DiarizeUtils.request_diarize(
+                url, data, headers, try_number=try_number + 1
+            )
+        else:
+            return res_json
+
+    def request_call_remaining(url, headers, try_number):
+        """
+        ------------------------------------------------------------------------------------------------------
+        Class: DiarizeUtils
+
+        Function: request_call_remaining
+
+        Description: This is an internal diarize function which makes a GET API call to brooklyn.health API server
+
+        Parameters:
+        ----------
+        url: The URL of the API endpoint.
+        headers: The headers to be sent in the request.
+        try_number: The number of times the function has been tried.
+
+        Returns:
+        ----------
+        json: The JSON response from the API server.
+        ------------------------------------------------------------------------------------------------------
+        """
+        try:
+            response = requests.get(url, headers=headers)
+            res_json = response.json()
+        except (
+            requests.exceptions.ConnectionError,
+            json.decoder.JSONDecodeError,
+        ) as ex:
+            if try_number == 3:
+                raise
+            time.sleep(random.random() * 2)
+            return DiarizeUtils.request_call_remaining(
+                url, headers, try_number=try_number + 1
+            )
+        else:
+            return res_json

willisapi_client-1.9.1/willisapi_client/services/diarize/willisdiarize.py

@@ -0,0 +1,52 @@
+from http import HTTPStatus
+
+from willisapi_client.willisapi_client import WillisapiClient
+from willisapi_client.logging_setup import logger as logger
+from willisapi_client.services.diarize.diarize_utils import DiarizeUtils
+
+
+def willis_diarize(key: str, file_path: str, **kwargs):
+    """
+    ---------------------------------------------------------------------------------------------------
+    Function: willis_diarize
+
+    Description: This function makes call to WillisDiarize Model
+
+    Parameters:
+    ----------
+    key: AWS access id token (str)
+    file_path: String
+
+    Returns:
+    ----------
+    json: JSON
+    ---------------------------------------------------------------------------------------------------
+    """
+
+    logger.info("Passing through WillisDiarize...")
+    wc = WillisapiClient(env=kwargs.get("env"))
+    url = wc.get_diarize()
+    headers = wc.get_headers()
+    headers["Authorization"] = key
+    corrected_transcript = None
+
+    if not DiarizeUtils.is_valid_file_path(file_path):
+        logger.info("Input file type is incorrect. We only accept JSON files.")
+        logger.info("Failed!")
+        return corrected_transcript
+
+    data = DiarizeUtils.read_json_file(file_path)
+
+    if not data:
+        return corrected_transcript
+
+    response = DiarizeUtils.request_diarize(url, data, headers, try_number=1)
+    if response["status_code"] != HTTPStatus.OK:
+        logger.info(response["message"])
+        logger.info("Failed!")
+    else:
+        logger.info("Returning processed JSON...")
+        encoded_response = response["data"]
+        corrected_transcript = DiarizeUtils.decode_response(encoded_response)
+        logger.info("Done!")
+    return corrected_transcript

willisapi_client-1.9.1/willisapi_client/services/diarize/willisdiarize_call_remaining.py

@@ -0,0 +1,28 @@
+from http import HTTPStatus
+
+from willisapi_client.willisapi_client import WillisapiClient
+from willisapi_client.logging_setup import logger as logger
+from willisapi_client.services.diarize.diarize_utils import DiarizeUtils
+
+
+def willis_diarize_call_remaining(key: str, **kwargs):
+    """
+    ---------------------------------------------------------------------------------------------------
+    Function: willis_diarize_call_remaining
+
+    Description: This function returns the number of remaining calls for willisdiarize
+
+    Parameters:
+    ----------
+    key: AWS access id token (str)
+    ---------------------------------------------------------------------------------------------------
+    """
+
+    wc = WillisapiClient(env=kwargs.get("env"))
+    url = wc.get_diarize_remaining_calls_url()
+    headers = wc.get_headers()
+    headers["Authorization"] = key
+
+    response = DiarizeUtils.request_call_remaining(url, headers, try_number=1)
+    if response:
+        logger.info(response["message"])

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client/services/download/download_utils.py

@@ -7,7 +7,7 @@ from typing import Tuple
 from http import HTTPStatus
 
 
-vocal_acoustic_summary = "vocal_acoustics_summary"
+vocal_acoustics_simple_summary = "vocal_acoustics_simple_summary"
 speech_characteristics_summary = "speech_characteristics_summary"
 rater_qa_summary = "rater_qa_summary"
 
@@ -91,6 +91,15 @@ class DownloadUtils:
         """
         return (
             response["project"]["participant"][pt]["participant_Id"],
+            response["project"]["participant"][pt]["age"],
+            response["project"]["participant"][pt]["sex"],
+            response["project"]["participant"][pt]["race"],
+            response["project"]["participant"][pt]["study_arm"],
+            response["project"]["participant"][pt]["clinical_score_a"],
+            response["project"]["participant"][pt]["clinical_score_b"],
+            response["project"]["participant"][pt]["clinical_score_c"],
+            response["project"]["participant"][pt]["clinical_score_d"],
+            response["project"]["participant"][pt]["clinical_score_e"],
             len(response["project"]["participant"][pt]["results"]),
         )
 
@@ -133,7 +142,21 @@ class DownloadUtils:
         column_names: A list of static column names of the dataframe
         ------------------------------------------------------------------------------------------------------
         """
-        return ["project_name", "pt_id_external", "filename", "time_collected"]
+        return [
+            "project_name",
+            "pt_id_external",
+            "filename",
+            "time_collected",
+            "age",
+            "sex",
+            "race",
+            "study_arm",
+            "clinical_score_a",
+            "clinical_score_b",
+            "clinical_score_c",
+            "clinical_score_d",
+            "clinical_score_e",
+        ]
 
     def _get_summary_df_from_json(response, pt, rec, workflow_tag):
         """
@@ -164,7 +187,7 @@ class DownloadUtils:
             and measures_dict[workflow_tag]
             and workflow_tag
             in [
-                vocal_acoustic_summary,
+                vocal_acoustics_simple_summary,
                 speech_characteristics_summary,
                 rater_qa_summary,
             ]
@@ -226,22 +249,48 @@ class DownloadUtils:
                 data
             )
             for pt in range(0, num_pts):
-                (pt_id_ext, num_records) = DownloadUtils._get_pt_id_ext_and_num_records(
-                    data, pt
-                )
+                (
+                    pt_id_ext,
+                    age,
+                    sex,
+                    race,
+                    study_arm,
+                    clinical_score_a,
+                    clinical_score_b,
+                    clinical_score_c,
+                    clinical_score_d,
+                    clinical_score_e,
+                    num_records,
+                ) = DownloadUtils._get_pt_id_ext_and_num_records(data, pt)
                 for rec in range(0, num_records):
                     (
                         filename,
                         time_collected,
                     ) = DownloadUtils._get_filename_and_timestamp(data, pt, rec)
                     main_df = pd.DataFrame(
-                        [[project_name, pt_id_ext, filename, time_collected]],
+                        [
+                            [
+                                project_name,
+                                pt_id_ext,
+                                filename,
+                                time_collected,
+                                age,
+                                sex,
+                                race,
+                                study_arm,
+                                clinical_score_a,
+                                clinical_score_b,
+                                clinical_score_c,
+                                clinical_score_d,
+                                clinical_score_e,
+                            ]
+                        ],
                         columns=DownloadUtils._get_defined_columns(),
                     )
 
-                    vocal_acoustics_summary_df = (
+                    vocal_acoustics_simple_summary_df = (
                         DownloadUtils._get_summary_df_from_json(
-                            data, pt, rec, vocal_acoustic_summary
+                            data, pt, rec, vocal_acoustics_simple_summary
                         )
                     )
                     speech_characteristics_summary_df = (
@@ -255,7 +304,7 @@ class DownloadUtils:
                     df = pd.concat(
                         [
                             main_df,
-                            vocal_acoustics_summary_df,
+                            vocal_acoustics_simple_summary_df,
                             speech_characteristics_summary_df,
                             rater_qa_summary_df,
                         ],

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client/services/upload/csv_validation.py

@@ -53,7 +53,7 @@ class CSVValidation:
         }
         self.gender_field = ["M", "F"]
         self.workflow_tags = [
-            "vocal_acoustics",
+            "vocal_acoustics_simple",
             "speech_characteristics",
             "speech_transcription_aws",
             "voice_and_speech",
@@ -71,6 +71,8 @@ class CSVValidation:
             "scale_",
             "speech_characteristics_",
             "rater_qa_",
+            "scale_wd_",
+            "rater_qa_wd_",
         ]
         self.collect_time_format = r"^\d{4}-\d{2}-\d{2}$"
         self.df = None

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client/services/upload/upload_utils.py

@@ -305,6 +305,7 @@ class UploadUtils:
         (upload_id, record_id, error) = UploadUtils.initiate_multi_part_upload(
             index, row, url, headers, force_upload
         )
+        filename = os.path.basename(row.file_path)
         uploaded = False
         if upload_id and record_id:
             presigned_urls, number_of_parts = UploadUtils.fetch_pre_signed_part_urls(
@@ -314,7 +315,7 @@ class UploadUtils:
                 if len(presigned_urls) != number_of_parts:
                     parts = json.dumps([])
                     res = requests.post(
-                        f"{url}?type=complete&record_id={record_id}&upload_id={upload_id}&number_of_parts={number_of_parts}",
+                        f"{url}?type=complete&record_id={record_id}&upload_id={upload_id}&number_of_parts={number_of_parts}&filename={filename}",
                         json=parts,
                         headers=headers,
                     )
@@ -324,7 +325,7 @@ class UploadUtils:
                     UploadUtils.close_file(file)
                     parts = json.dumps(parts)
                     res = requests.post(
-                        f"{url}?type=complete&record_id={record_id}&upload_id={upload_id}&number_of_parts={number_of_parts}",
+                        f"{url}?type=complete&record_id={record_id}&upload_id={upload_id}&number_of_parts={number_of_parts}&filename={filename}",
                         json=parts,
                         headers=headers,
                     )

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client/willisapi_client.py

@@ -25,14 +25,17 @@ class WillisapiClient:
     def get_login_url(self):
         return self.get_base_url() + "login"
 
-    def get_signup_url(self):
-        return self.get_base_url() + "signup"
-
     def get_upload_url(self):
         return self.get_base_url() + "upload"
 
     def get_download_url(self):
         return self.get_base_url() + "download"
 
+    def get_diarize_remaining_calls_url(self):
+        return self.get_base_url() + "willis-diarize-call-remaining"
+
+    def get_diarize(self):
+        return self.get_base_url() + "diarize"
+
     def get_headers(self):
         return {"Content-Type": "application/json", "Accept": "application/json"}

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: willisapi-client
-Version: 1.8
+Version: 1.9.1
 Summary: A Python client for willisapi
 Home-page: https://github.com/bklynhlth/willsiapi_client
 Author: bklynhlth
@@ -39,7 +39,7 @@ Conversion notes:
 
 WillisAPI Client is the python interface for Brooklyn Health’s WillisAPI.
 
-Official documentation for WillisAPI Client can be found in the [Github Wiki](www.github.com/bklynhlth/willisapi_client/wiki).
+Official documentation for WillisAPI Client can be found in the [Github Wiki](http://www.github.com/bklynhlth/willisapi_client/wiki).
 
 To learn more about Brooklyn Health or WillisAPI, visit [brooklyn.health](https://www.brooklyn.health) or [getintouch@brooklyn.health](mailto:getintouch@brooklyn.health).
 
@@ -82,10 +82,10 @@ measures = willisapi.download(key, 'project_name')
 ```
 
 
-If you run into trouble while using the client, please raise it in the [Issues](www.github.com/bklynhlth/willisapi_client/issues) tab. 
+If you run into trouble while using the client, please raise it in the [Issues](http://www.github.com/bklynhlth/willisapi_client/issues) tab. 
 
 ***
 
 Brooklyn Health is a small team of clinicians, scientists, and engineers based in Brooklyn, NY. 
 
-We develop and maintain [OpenWillis](www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 
+We develop and maintain [OpenWillis](http://www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 

{willisapi_client-1.8 → willisapi_client-1.9.1}/willisapi_client.egg-info/SOURCES.txt

@@ -7,6 +7,8 @@ setup.cfg
 setup.py
 tests/test_auth.py
 tests/test_csv_validation.py
+tests/test_diarize.py
+tests/test_diarize_call_remaining.py
 tests/test_download.py
 tests/test_upload.py
 willisapi_client/__init__.py
@@ -26,6 +28,10 @@ willisapi_client/services/exceptions.py
 willisapi_client/services/auth/__init__.py
 willisapi_client/services/auth/auth_utils.py
 willisapi_client/services/auth/login_manager.py
+willisapi_client/services/diarize/__init__.py
+willisapi_client/services/diarize/diarize_utils.py
+willisapi_client/services/diarize/willisdiarize.py
+willisapi_client/services/diarize/willisdiarize_call_remaining.py
 willisapi_client/services/download/__init__.py
 willisapi_client/services/download/download_handler.py
 willisapi_client/services/download/download_utils.py

willisapi_client-1.8/willisapi_client/__init__.py

@@ -1,10 +0,0 @@
-# website:   https://www.brooklyn.health
-
-# import the required packages
-from willisapi_client.services.api import (
-    login,
-    upload,
-    download,
-)
-
-__all__ = ["login", "upload", "download"]