switch stray components to bytes

osm/pipeline/core.py

@@ -15,7 +15,7 @@ def __init__(self, version: str = "0.0.1"):
         self._orm_model = None
 
     @abstractmethod
-    def _run(self, data: bytes, **kwargs) -> Any:
+    def _run(self, data: bytes|dict, **kwargs) -> Any:
         """Abstract method that subclasses must implement."""
         pass
 
@@ -64,7 +64,7 @@ def __iter__(self):
         yield self.json_saver
         yield self.osm_saver
 
-    def save_file(self, data: str, path: Path):
+    def save_file(self, data: bytes, path: Path):
         self.file_saver.run(data, path=path)
 
     def save_json(self, data: dict, path: Path):
@@ -102,7 +102,7 @@ def __init__(
     def run(self):
         for parser in self.parsers:
             parsed_data = parser.run(self.file_data)
-            if isinstance(parsed_data, str):
+            if isinstance(parsed_data, bytes):
                 self.savers.save_file(parsed_data, self.xml_path)
             for extractor in self.extractors:
                 extracted_metrics = extractor.run(parsed_data, parser=parser.name)

osm/pipeline/parsers.py

@@ -3,6 +3,7 @@
 from osm.schemas.custom_fields import LongBytes
 
 from .core import Component
+import io
 
 SCIENCEBEAM_URL = "http://localhost:8070/api/convert"
 
@@ -30,8 +31,10 @@ class ScienceBeamParser(Component):
     def _run(self, data: bytes) -> str:
         self.sample = LongBytes(data)
         headers = {"Accept": "application/tei+xml", "Content-Type": "application/pdf"}
-        response = requests.post(SCIENCEBEAM_URL, data=data, headers=headers)
+        files = {'file': ('input.pdf', io.BytesIO(data), 'application/pdf')}
+
+        response = requests.post(SCIENCEBEAM_URL, files=files, headers=headers)
         if response.status_code == 200:
-            return response.text
+            return response.content
         else:
             response.raise_for_status()

osm/pipeline/savers.py

@@ -27,14 +27,14 @@ def format_error_message() -> str:
 class FileSaver(Component):
     """Basic saver that writes data to a file."""
 
-    def _run(self, data: str, path: Path):
+    def _run(self, data: bytes, path: Path):
         """Write data to a file.
 
         Args:
             data (str): Some data.
             path (Path): A file path.
         """
-        path.write_text(data)
+        path.write_bytes(data)
         logger.info(f"Data saved to {path}")