fix: update tox envlist, add ruff for linting and formatting, set up …

…pre-commit, and clean up code (docker, server) before XML conversion

README.md

@@ -9,6 +9,8 @@ Windows: `venv\Scripts\activate`<br>
 macOS and Linux: `source venv/bin/activate`
 
 - Next, run `pip install -e .` to install the package with its dependencies.
+- Open a terminal tab and run the image `docker run --rm -p 8082:8070 elifesciences/sciencebeam-parser` and keep it running for the rest of the testing period
+- Go back to terminal(root folder)
 - Finally, run `osm pdf-xml "path_to_file_name.pdf" file_id`
 
 # How to run tests of the application

osm/cli/main.py

@@ -23,9 +23,17 @@ def pdf_xml(file_path, file_id):
     """
     try:
         converter = PDFConverter()
+
+        if not converter.is_docker_running():
+            raise click.ClickException('Please make sure the docker is running')
+
+        if not converter.is_host_ready():
+            raise click.ClickException('The converter server is offline')
+
         xml_content = converter.convert(file_path)
         # Save the converted xml contents
-        with open(f'docs/examples/sci`encebeam_xml_outputs/{file_id}.xml', 'w', encoding='utf-8') as xml_file:
+        output_file: str = f'docs/examples/sciencebeam_xml_outputs/{file_id}.xml'
+        with open(output_file, 'w', encoding='utf-8') as xml_file:
             xml_file.write(xml_content)
             logger.info(f'Converted: {file_path} with ID: {file_id} to XML')
 

osm/converters/pdf_converter.py

@@ -1,26 +1,62 @@
+import socket
+
+import docker
+from docker.errors import DockerException
 from pydantic import FilePath
 import requests
 
 from osm_cli.converters.converter import Converter
+from osm_cli.utils.config import config
 
 
 class PDFConverter(Converter):
-    sciencebeam_url: str = 'http://localhost:8080/api/convert'
+    protocol: str = config.PROTOCAL
+    host: str = config.HOST
+    port: int = config.PORT
 
-    def convert(self, pdf_path: FilePath):
+    def convert(self, pdf_path: FilePath) -> str:
         """Convert a PDF file to XML using ScienceBeam Parser.
 
         Args:
             pdf_path: Path to the PDF file
         Returns:
             XML content as a string
         """
+        sciencebeam_url: str = f'{self.protocol}://{self.host}:{self.port}/api/convert'
         with open(pdf_path, 'rb') as pdf_file:
             files = {'file': pdf_file}
             headers = {'Accept': 'application/tei+xml'}
-            response = requests.post(self.sciencebeam_url, files=files, headers=headers)
+            response = requests.post(
+                sciencebeam_url, files=files, headers=headers)
 
             if response.status_code == 200:
                 return response.text
             else:
                 response.raise_for_status()
+
+    def is_host_ready(self, timeout=3) -> bool:
+        """Check if the host is ready to accept requests.
+        Args:
+            timeout: Timeout in seconds
+        Returns:
+            True if the docker is host is ready, False otherwise
+        """
+        with socket.socket(socket.AF_INET, socket.SOCK_STREAM) as sock:
+            sock.settimeout(timeout)
+            try:
+                sock.connect((self.host, self.port))
+            except (socket.timeout, socket.error):
+                return False
+            return True
+
+    def is_docker_running(self):
+        """Check if the docker image exists.
+        Returns:
+            True if the docker image exists, False otherwise
+        """
+        try:
+            client = docker.from_env()
+            client.images.get('elifesciences/sciencebeam-parser')
+            return True
+        except DockerException:
+            return False