willisapi-client 1.9.2__tar.gz → 1.9.3__tar.gz

willisapi_client-1.9.3/PKG-INFO

@@ -0,0 +1,119 @@
+Metadata-Version: 2.1
+Name: willisapi_client
+Version: 1.9.3
+Summary: A Python client for willisapi
+Home-page: https://github.com/bklynhlth/willsiapi_client
+Author: bklynhlth
+Author-email: admin@brooklyn.health
+License: Apache
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+<!-- Output copied to clipboard! -->
+
+<!-----
+
+Yay, no errors, warnings, or alerts!
+
+Conversion time: 0.36 seconds.
+
+
+Using this Markdown file:
+
+1. Paste this output into your source file.
+2. See the notes and action items below regarding this conversion run.
+3. Check the rendered output (headings, lists, code blocks, tables) for proper
+   formatting and use a linkchecker before you publish this page.
+
+Conversion notes:
+
+* Docs to Markdown version 1.0β34
+* Mon Aug 21 2023 13:41:56 GMT-0700 (PDT)
+* Source doc: README.md
+----->
+
+
+
+### WillisAPI Client
+
+WillisAPI Client is the Python interface for Brooklyn Health’s WillisAPI.
+
+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).
+
+---
+
+#### Installation
+
+
+```bash
+pip install willisapi_client
+```
+
+---
+
+#### Getting a Personal Access Token (PAT)
+1. Log in to the Brooklyn Health web application.
+2. Go to your profile section.
+3. Navigate to Personal Access Token (PAT) and copy it for use in the client.
+
+---
+
+#### Usage
+
+**Upload**
+To upload a CSV file:
+
+```python
+summary = willisapi.upload(key, '/path/to/data.csv')
+```
+
+How to Call the Function
+- key: Your PAT token.
+- data.csv: Path to your CSV file.
+
+How to Reupload
+
+If you need to reupload the same or updated file, simply call the upload function again:
+
+```python
+summary = willisapi.upload(key, 'data.csv', force_uploade=True)
+```
+---
+#### Understanding Returned DataFrame and Errors
+
+- The upload function returns a summary DataFrame containing the results of your upload.
+- Columns typically include status, error messages, and metadata for each row in your CSV.
+- If there are errors, they will be listed in the DataFrame under an error or message column.
+- Review the DataFrame to identify and resolve any issues before reuploading.
+
+---
+
+#### CSV Validation Details
+
+Before uploading, the client validates your CSV for:
+
+- **Required Columns**: Must include study_id, site_id, rater_email, participant_id, visit_name, visit_order, coa_name, coa_item_number, coa_item_value, file_path, time_collected.
+- **Optional Columns**: age, sex, race, language.
+- **Valid COA Name**: Only these values are allowed: MADRS, YMRS, PHQ-9, GAD-7.
+- **Valid Audio File**: The file path in each row must exist and be accessible.
+- **Valid Email**: rater_email must be a valid email.
+- **Valid Data Types**: visit_order, age, coa_item_number, and coa_item_value must be numeric.
+- **Language**: If present, must be in the allowed language choices.
+
+If any validation fails, errors are collected and returned for review before upload proceeds.
+
+---
+
+For more information on how to organize the `data.csv`, visit the [Github Wiki](http://www.github.com/bklynhlth/willisapi_client/wiki).
+
+
+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](http://www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 

willisapi_client-1.9.3/README.md

@@ -0,0 +1,107 @@
+<!-- Output copied to clipboard! -->
+
+<!-----
+
+Yay, no errors, warnings, or alerts!
+
+Conversion time: 0.36 seconds.
+
+
+Using this Markdown file:
+
+1. Paste this output into your source file.
+2. See the notes and action items below regarding this conversion run.
+3. Check the rendered output (headings, lists, code blocks, tables) for proper
+   formatting and use a linkchecker before you publish this page.
+
+Conversion notes:
+
+* Docs to Markdown version 1.0β34
+* Mon Aug 21 2023 13:41:56 GMT-0700 (PDT)
+* Source doc: README.md
+----->
+
+
+
+### WillisAPI Client
+
+WillisAPI Client is the Python interface for Brooklyn Health’s WillisAPI.
+
+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).
+
+---
+
+#### Installation
+
+
+```bash
+pip install willisapi_client
+```
+
+---
+
+#### Getting a Personal Access Token (PAT)
+1. Log in to the Brooklyn Health web application.
+2. Go to your profile section.
+3. Navigate to Personal Access Token (PAT) and copy it for use in the client.
+
+---
+
+#### Usage
+
+**Upload**
+To upload a CSV file:
+
+```python
+summary = willisapi.upload(key, '/path/to/data.csv')
+```
+
+How to Call the Function
+- key: Your PAT token.
+- data.csv: Path to your CSV file.
+
+How to Reupload
+
+If you need to reupload the same or updated file, simply call the upload function again:
+
+```python
+summary = willisapi.upload(key, 'data.csv', force_uploade=True)
+```
+---
+#### Understanding Returned DataFrame and Errors
+
+- The upload function returns a summary DataFrame containing the results of your upload.
+- Columns typically include status, error messages, and metadata for each row in your CSV.
+- If there are errors, they will be listed in the DataFrame under an error or message column.
+- Review the DataFrame to identify and resolve any issues before reuploading.
+
+---
+
+#### CSV Validation Details
+
+Before uploading, the client validates your CSV for:
+
+- **Required Columns**: Must include study_id, site_id, rater_email, participant_id, visit_name, visit_order, coa_name, coa_item_number, coa_item_value, file_path, time_collected.
+- **Optional Columns**: age, sex, race, language.
+- **Valid COA Name**: Only these values are allowed: MADRS, YMRS, PHQ-9, GAD-7.
+- **Valid Audio File**: The file path in each row must exist and be accessible.
+- **Valid Email**: rater_email must be a valid email.
+- **Valid Data Types**: visit_order, age, coa_item_number, and coa_item_value must be numeric.
+- **Language**: If present, must be in the allowed language choices.
+
+If any validation fails, errors are collected and returned for review before upload proceeds.
+
+---
+
+For more information on how to organize the `data.csv`, visit the [Github Wiki](http://www.github.com/bklynhlth/willisapi_client/wiki).
+
+
+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](http://www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 

{willisapi_client-1.9.2 → willisapi_client-1.9.3}/willisapi_client/__init__.py

@@ -2,19 +2,13 @@
 
 # import the required packages
 from willisapi_client.services.api import (
-    login,
-    upload,
-    download,
     willis_diarize_call_remaining,
     willis_diarize,
-    metadata_upload,
+    upload,
 )
 
 __all__ = [
-    "login",
-    "upload",
-    "download",
     "willis_diarize_call_remaining",
     "willis_diarize",
-    "metadata_upload",
+    "upload",
 ]

{willisapi_client-1.9.2 → willisapi_client-1.9.3}/willisapi_client/__version__.py

@@ -1,7 +1,7 @@
 """Version details for willisapi_client"""
 
 __client__ = "willisapi_client"
-__latestVersion__ = "1.9.2"
+__latestVersion__ = "1.9.3"
 __url__ = "https://github.com/bklynhlth/willsiapi_client"
 __short_description__ = "A Python client for willisapi"
 __content_type__ = "text/markdown"

willisapi_client-1.9.3/willisapi_client/services/api.py

@@ -0,0 +1,8 @@
+# website:   https://www.brooklyn.health
+
+# import the required packages
+from willisapi_client.services.diarize import (
+    willis_diarize_call_remaining,
+    willis_diarize,
+)
+from willisapi_client.services.metadata import upload

willisapi_client-1.9.3/willisapi_client/services/metadata/__init__.py

@@ -0,0 +1,4 @@
+# website:   https://www.brooklyn.health
+from .upload import upload
+
+__all__ = ["upload"]

{willisapi_client-1.9.2 → willisapi_client-1.9.3}/willisapi_client/services/metadata/upload.py

@@ -2,6 +2,7 @@ import pandas as pd
 from tqdm import tqdm
 from datetime import datetime
 import requests
+import mimetypes
 
 from willisapi_client.timer import measure
 from willisapi_client.willisapi_client import WillisapiClient
@@ -10,7 +11,7 @@ from willisapi_client.services.metadata.utils import MetadataValidation, UploadU
 
 
 @measure
-def metadata_upload(api_key: str, csv_path: str, **kwargs):
+def upload(api_key: str, csv_path: str, **kwargs):
 
     force_upload = kwargs.get("force_upload", False)
     csv = MetadataValidation(csv_path=csv_path, force_upload=force_upload)
@@ -19,7 +20,7 @@ def metadata_upload(api_key: str, csv_path: str, **kwargs):
         csv.create_final_csv()
 
         wc = WillisapiClient(env=kwargs.get("env"))
-        url = wc.get_metadata_upload_url()
+        url = wc.get_upload_url()
         headers = wc.get_headers()
         headers["Authorization"] = f"token {api_key}"
         logger.info(f'{datetime.now().strftime("%H:%M:%S")}: beginning upload')
@@ -42,12 +43,22 @@ def metadata_upload(api_key: str, csv_path: str, **kwargs):
                     presigned = res.get("response", {}).get("presigned")
                     if presigned:
                         try:
+                            content_type, _ = mimetypes.guess_type(
+                                payload.get("filename")
+                            )
+                            if not content_type:
+                                content_type = "application/octet-stream"
                             with open(row.file_path, "rb") as f:
-                                files = {"file": f}
                                 response = requests.put(
                                     presigned,
-                                    data=files["file"],
-                                    headers={"Content-Type": "audio/ogg"},
+                                    data=f,
+                                    headers={
+                                        "x-amz-checksum-sha256": payload.get(
+                                            "checksum"
+                                        ),
+                                        "x-amz-sdk-checksum-algorithm": "SHA256",
+                                        "Content-Type": content_type,
+                                    },
                                 )
                             if response.status_code == 200:
                                 result_row["upload_status"] = "Success"
@@ -73,11 +84,8 @@ def metadata_upload(api_key: str, csv_path: str, **kwargs):
             results.append(result_row)
 
         results_df = pd.DataFrame(results)
-        results_df.to_csv(
-            f"metadata_upload_results_{datetime.now().strftime('%Y%m%d_%H%M%S')}.csv",
-            index=False,
-        )
         return results_df
     else:
         logger.error(f'{datetime.now().strftime("%H:%M:%S")}: csv check failed')
+        logger.error(csv.errors)
         return None

{willisapi_client-1.9.2 → willisapi_client-1.9.3}/willisapi_client/services/metadata/utils.py

@@ -2,8 +2,10 @@ import pandas as pd
 from typing import List, Dict, Any, Tuple
 import json
 import os
+import hashlib
+import base64
 import requests
-from willisapi_client.services.upload.language_choices import (
+from .language_choices import (
     LANGUAGE_CHOICES,
 )
 
@@ -293,13 +295,24 @@ class UploadUtils:
     def __init__(self, row):
         self.row = row
 
-    def validate_row(self) -> Tuple[bool, str | None]:
+    def validate_row(self):
         if not os.path.exists(self.row.file_path):
             return (False, "File path does not exist")
         if self.row.language not in LANGUAGE_CHOICES:
             return (False, f"Invalid language: {self.row.language}")
         return (True, None)
 
+    def calculate_file_checksum(self, file_path: str) -> str:
+        try:
+            with open(file_path, "rb") as f:
+                file_data = f.read()
+
+            hash_bytes = hashlib.sha256(file_data).digest()
+            base64_hash = base64.b64encode(hash_bytes).decode("utf-8")
+            return base64_hash
+        except Exception as e:
+            raise RuntimeError(f"Failed to calculate checksum: {e}")
+
     def generate_payload(self) -> Dict[str, Any]:
         payload = {
             "study_id": self.row.study_id,
@@ -317,6 +330,7 @@ class UploadUtils:
             "filename": os.path.basename(self.row.file_path),
             "force_upload": self.row.force_upload,
             "actual_scores": json.loads(self.row.actual_scores),
+            "checksum": self.calculate_file_checksum(self.row.file_path),
         }
         return payload
 

{willisapi_client-1.9.2 → willisapi_client-1.9.3}/willisapi_client/willisapi_client.py

@@ -27,22 +27,13 @@ class WillisapiClient:
             return f"https://{self.env}-{self.api_uri}/api/v2/"
         return f"https://{self.api_uri}/api/v2/"
 
-    def get_login_url(self):
-        return self.get_base_url() + "login"
-
-    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_metadata_upload_url(self):
+    def get_upload_url(self):
         return self.get_base_v2_url() + "metadata/upload"
 
     def get_headers(self):

willisapi_client-1.9.3/willisapi_client.egg-info/PKG-INFO

@@ -0,0 +1,119 @@
+Metadata-Version: 2.1
+Name: willisapi-client
+Version: 1.9.3
+Summary: A Python client for willisapi
+Home-page: https://github.com/bklynhlth/willsiapi_client
+Author: bklynhlth
+Author-email: admin@brooklyn.health
+License: Apache
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+<!-- Output copied to clipboard! -->
+
+<!-----
+
+Yay, no errors, warnings, or alerts!
+
+Conversion time: 0.36 seconds.
+
+
+Using this Markdown file:
+
+1. Paste this output into your source file.
+2. See the notes and action items below regarding this conversion run.
+3. Check the rendered output (headings, lists, code blocks, tables) for proper
+   formatting and use a linkchecker before you publish this page.
+
+Conversion notes:
+
+* Docs to Markdown version 1.0β34
+* Mon Aug 21 2023 13:41:56 GMT-0700 (PDT)
+* Source doc: README.md
+----->
+
+
+
+### WillisAPI Client
+
+WillisAPI Client is the Python interface for Brooklyn Health’s WillisAPI.
+
+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).
+
+---
+
+#### Installation
+
+
+```bash
+pip install willisapi_client
+```
+
+---
+
+#### Getting a Personal Access Token (PAT)
+1. Log in to the Brooklyn Health web application.
+2. Go to your profile section.
+3. Navigate to Personal Access Token (PAT) and copy it for use in the client.
+
+---
+
+#### Usage
+
+**Upload**
+To upload a CSV file:
+
+```python
+summary = willisapi.upload(key, '/path/to/data.csv')
+```
+
+How to Call the Function
+- key: Your PAT token.
+- data.csv: Path to your CSV file.
+
+How to Reupload
+
+If you need to reupload the same or updated file, simply call the upload function again:
+
+```python
+summary = willisapi.upload(key, 'data.csv', force_uploade=True)
+```
+---
+#### Understanding Returned DataFrame and Errors
+
+- The upload function returns a summary DataFrame containing the results of your upload.
+- Columns typically include status, error messages, and metadata for each row in your CSV.
+- If there are errors, they will be listed in the DataFrame under an error or message column.
+- Review the DataFrame to identify and resolve any issues before reuploading.
+
+---
+
+#### CSV Validation Details
+
+Before uploading, the client validates your CSV for:
+
+- **Required Columns**: Must include study_id, site_id, rater_email, participant_id, visit_name, visit_order, coa_name, coa_item_number, coa_item_value, file_path, time_collected.
+- **Optional Columns**: age, sex, race, language.
+- **Valid COA Name**: Only these values are allowed: MADRS, YMRS, PHQ-9, GAD-7.
+- **Valid Audio File**: The file path in each row must exist and be accessible.
+- **Valid Email**: rater_email must be a valid email.
+- **Valid Data Types**: visit_order, age, coa_item_number, and coa_item_value must be numeric.
+- **Language**: If present, must be in the allowed language choices.
+
+If any validation fails, errors are collected and returned for review before upload proceeds.
+
+---
+
+For more information on how to organize the `data.csv`, visit the [Github Wiki](http://www.github.com/bklynhlth/willisapi_client/wiki).
+
+
+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](http://www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement. 

{willisapi_client-1.9.2 → willisapi_client-1.9.3}/willisapi_client.egg-info/SOURCES.txt

@@ -5,12 +5,8 @@ RELEASE.md
 requirements.txt
 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
 willisapi_client/__version__.py
 willisapi_client/logging_setup.py
@@ -25,22 +21,11 @@ willisapi_client.egg-info/top_level.txt
 willisapi_client/services/__init__.py
 willisapi_client/services/api.py
 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/services/metadata/__init__.py
+willisapi_client/services/metadata/language_choices.py
 willisapi_client/services/metadata/upload.py
-willisapi_client/services/metadata/utils.py
-willisapi_client/services/upload/__init__.py
-willisapi_client/services/upload/csv_validation.py
-willisapi_client/services/upload/language_choices.py
-willisapi_client/services/upload/multipart_upload_handler.py
-willisapi_client/services/upload/upload_utils.py
-willisapi_client/services/upload/utils.py
+willisapi_client/services/metadata/utils.py

willisapi_client-1.9.2/PKG-INFO

@@ -1,83 +0,0 @@
-Metadata-Version: 2.1
-Name: willisapi_client
-Version: 1.9.2
-Summary: A Python client for willisapi
-Home-page: https://github.com/bklynhlth/willsiapi_client
-Author: bklynhlth
-Author-email: admin@brooklyn.health
-License: Apache
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-<!-- Output copied to clipboard! -->
-
-<!-----
-
-Yay, no errors, warnings, or alerts!
-
-Conversion time: 0.36 seconds.
-
-
-Using this Markdown file:
-
-1. Paste this output into your source file.
-2. See the notes and action items below regarding this conversion run.
-3. Check the rendered output (headings, lists, code blocks, tables) for proper
-   formatting and use a linkchecker before you publish this page.
-
-Conversion notes:
-
-* Docs to Markdown version 1.0β34
-* Mon Aug 21 2023 13:41:56 GMT-0700 (PDT)
-* Source doc: README.md
------>
-
-
-
-### WillisAPI Client
-
-WillisAPI Client is the python interface for Brooklyn Health’s WillisAPI.
-
-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).
-
-
-#### Installation
-
-
-```
-pip install willisapi_client
-```
-
-
-**Login**
-
-Before you log in, make sure you have an account with Brooklyn Health.
-
-
-```
-import willisapi_client as willisapi
-key, expiration = willisapi.login(username, password)
-```
-
-
-**Upload**
-
-
-```
-summary = willisapi.metadata_upload(key, 'data.csv')
-```
-
-
-For more information on how to organize the `data.csv`, visit the [Github Wiki](http://www.github.com/bklynhlth/willisapi_client/wiki).
-
-
-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](http://www.github.com/bklynhlth/openwillis), an open source python library for digital health measurement.