updated the pysysrev package

.github/workflows/pypi_publish.yml

@@ -0,0 +1,31 @@
+name: Publish Python package to PyPI
+
+on:
+  push:
+    branches:
+      - master  # Set this to your default branch
+
+jobs:
+  build-and-publish:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.9'  # Use the Python version compatible with your project
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish to PyPI
+        if: github.event_name == 'push' && startsWith(github.ref, 'refs/heads/master')
+        uses: pypa/[email protected]
+        with:
+          password: ${{ secrets.PYPI_TOKEN }}
+          user: sysrev

.github/workflows/sysrev.yml.old

@@ -0,0 +1,23 @@
+name: Biobricks codecov
+
+on: [push, pull_request]
+
+env:
+  BIOBRICKS_TEST_TOKEN: ${{ secrets.BIOBRICKS_TEST_TOKEN }}
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Test biobricks
+    steps:
+      - uses: actions/checkout@v2  # Updated to use v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: '3.10'
+      - name: Install requirements
+        run: pip install -r requirements.txt  # Removed the working-directory override for this step
+      - name: Run tests and collect coverage
+        run: pytest --cov=./ --cov-report=xml
+        working-directory: ./  # Set the working directory only for the test step
+      - name: Upload coverage reports to Codecov with GitHub Action
+        uses: codecov/codecov-action@v3

README

@@ -1,9 +1,4 @@
-A Python client for sysrev.com
-
-See Demo.ipynb for implementation of client on example project.
-
-To install PySysrev, simply run `pip install PySysrev`
-
-Then inside Python, run the following commands:
->>> import PySysrev
->>> df = PySysrev.getAnnotations(3144)
+# Sysrev Python Client
+The Sysrev package provides:
+1. `SysrevClient` object for using the sysrev.com API
+2. (soon) a method for synchronizing local sysrev projects with remote sysrev projects.

setup.py

@@ -1,12 +1,12 @@
 from setuptools import setup
 
-setup(name='PySysrev',
-      version='1.2.1',
+setup(name='sysrev',
+      version='1.2.2',
       description='Gets annotations from Sysrev API',
       url='https://github.com/sysrev/PySysrev',
-      author='nole-lin',
-      author_email='nole@insilica.co',
-      packages=['PySysrev'],
+      author='Thomas Luechtefeld',
+      author_email='tom@insilica.co',
+      packages=['sysrev'],
       install_requires=[
           'pandas',
           'requests',

sysrev/__init__.py

@@ -0,0 +1 @@
+from .funcs import SysrevClient

sysrev/funcs.py

@@ -0,0 +1,103 @@
+import requests
+
+class LabelTransformer:
+
+    def handle_boolean(self, label_value):
+        if isinstance(label_value, bool):
+            return label_value
+        elif str(label_value).lower() in ['yes', 'no']:
+            return str(label_value).lower() == 'yes'
+        else:
+            raise ValueError("Invalid boolean value")
+
+    def handle_categorical_or_string(self, label_value):
+        if isinstance(label_value, str):
+            return [label_value]
+        elif isinstance(label_value, list) and all(isinstance(item, str) for item in label_value):
+            return label_value
+        else:
+            raise ValueError("Invalid value for categorical or string type")
+
+    def transform_label(self, label_type, label_value):
+        if label_type == 'boolean':
+            return self.handle_boolean(label_value)
+        elif label_type in ['categorical', 'string']:
+            return self.handle_categorical_or_string(label_value)
+        else:
+            raise ValueError("Invalid label type")
+
+class SysrevClient():
+
+    def __init__(self, api_key, base_url="https://www.sysrev.com"):
+        self.api_key = api_key
+        self.base_url = base_url
+
+    def get_project_info(self, project_id):
+        endpoint = f"{self.base_url}/api-json/project-info"
+        headers = {"Authorization": f"Bearer {self.api_key}"}
+        response = requests.get(endpoint, headers=headers, params={"project-id": project_id})
+        return response.json()
+
+    def set_labels(self, project_id, article_id, label_ids, label_values, label_types, confirm=False, change=False, resolve=False):
+        endpoint = f"{self.base_url}/api-json/set-labels"
+        headers = {"Authorization": f"Bearer {self.api_key}", "Content-Type": "application/json"}
+
+        assert len(label_ids) == len(label_values) == len(label_types), "Length of label_ids, label_values, and label_types should be the same."
+
+        # construct label_values_dict
+        tf = LabelTransformer()
+        label_values_dict = {label_ids[i]: tf.transform_label(label_types[i], label_values[i]) for i in range(len(label_ids))}    
+
+        # Constructing the data payload as per the server's expectation
+        data = {"project-id": project_id, "article-id": article_id, "label-values": label_values_dict}
+        data.update({ "confirm?": confirm, "change?": change, "resolve?": resolve })
+
+        # Sending a POST request to the server
+        response = requests.post(endpoint, json=data, headers=headers)
+        return response.json()
+
+    def get_project_articles(self, project_id, offset=0, limit=10, sort_by=None, sort_dir=None):
+        endpoint = f"{self.base_url}/api-json/project-articles"
+        headers = {"Authorization": f"Bearer {self.api_key}", "Content-Type": "application/json"}
+        body = {"project-id": project_id, "n-offset": offset, "n-count": limit}
+
+        # Add optional sorting keys if provided
+        if sort_by: body["sort-by"] = sort_by
+        if sort_dir: body["sort-dir"] = sort_dir
+
+        # Make the POST request with the simplified body
+        response = requests.post(endpoint, headers=headers, json=body)
+        return response.json()
+
+    def fetch_all_articles(self, project_id, limit=10, sort_by=None, sort_dir=None):
+        offset = 0
+        while True:
+            result = self.get_project_articles(project_id, offset=offset, limit=limit, sort_by=sort_by, sort_dir=sort_dir)
+            articles = result.get('result', [])
+            if not articles:
+                break  # Stop iteration if no articles are left
+            yield from articles  # Yield each article in the current batch
+            offset += len(articles)
+
+    def get_article_info(self, project_id, article_id):
+        endpoint = f"{self.base_url}/api-json/article-info/{article_id}"
+        headers = {"Authorization": f"Bearer {self.api_key}", "Content-Type": "application/json"}
+        body = {"project-id": project_id,}
+        return requests.get(endpoint, headers=headers, json=body)
+
+    def upload_jsonlines(self, file_path, project_id):
+        url = f"{self.base_url}/api-json/import-files/{project_id}"
+        headers = {"Authorization": f"Bearer {self.api_key}"}
+
+        # Prepare the file for upload
+        with open(file_path, 'rb') as f:
+            files = {'file': (file_path.split('/')[-1], f, 'application/octet-stream')}
+            # Let requests handle "Content-Type"
+            response = requests.post(url, headers=headers, files=files)
+
+        return response
+
+    def get_article_file(self, project_id, article_id, hash):
+        url = f"{self.base_url}/api-json/files/{project_id}/article/{article_id}/download/{hash}"
+        headers = {"Authorization": f"Bearer {self.api_key}", "Content-Type": "application/json"}
+