Merge pull request #31 from tstoeter/main

Author: joshmoore

src/omero_rdf/__init__.py

@@ -19,6 +19,9 @@
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
 
 
+import contextlib
+import gzip
+import sys
 import json
 import logging
 from argparse import Namespace
@@ -36,19 +39,24 @@
 from rdflib.namespace import DCTERMS, RDF
 from rdflib_pyld_compat import pyld_jsonld_from_rdflib_graph
 
-HELP = """A plugin for exporting rdf from OMERO
+HELP = """A plugin for exporting RDF from OMERO
 
 omero-rdf creates a stream of RDF triples from the starting object that
 it is given. This may be one of: Image, Dataset, Project, Plate, and Screen.
 
 Examples:
 
   omero rdf Image:123                # Streams each triple found in N-Triples format
+
   omero rdf -F=jsonld Image:123      # Collects all triples and prints formatted output
   omero rdf -S=flat Project:123      # Do not recurse into containers ("flat-strategy")
   omero rdf --trim-whitespace ...    # Strip leading and trailing whitespace from text
   omero rdf --first-handler-wins ... # First mapping wins; others will be ignored
 
+  omero rdf --file - ...             # Write RDF triples to stdout
+  omero rdf --file output.nt ...     # Write RDF triples to the specified file
+  omero rdf --file output.nt.gz      # Write RDF triples to the specified file, gzipping
+
 """
 
 # TYPE DEFINITIONS
@@ -60,6 +68,37 @@
 Handlers = List[Callable[[URIRef, URIRef, Data], Generator[Triple, None, bool]]]
 
 
+@contextlib.contextmanager
+def open_with_default(filename=None, filehandle=None):
+    """
+    Open a file for writing if given and close on completion.
+
+    No closing will happen if the file name is "-" since stdout will be used.
+    If no filehandle is given, stdout will also be used.
+    Otherwise return the given filehandle will be used.
+    """
+    close = False
+    if filename:
+        if filename == "-":
+            fh = sys.stdout
+        else:
+            if filename.endswith(".gz"):
+                fh = gzip.open(filename, "wt")
+            else:
+                fh = open(filename, "w")
+            close = True
+    else:
+        if filehandle is None:
+            filehandle = sys.stdout
+        fh = filehandle
+
+    try:
+        yield fh
+    finally:
+        if close:
+            fh.close()
+
+
 def gateway_required(func: Callable) -> Callable:  # type: ignore
     """
     Decorator which initializes a client (self.client),
@@ -256,6 +295,7 @@ def __init__(
         use_ellide=False,
         first_handler_wins=False,
         descent="recursive",
+        filehandle=sys.stdout,
     ) -> None:
         self.gateway = gateway
         self.cache: Set[URIRef] = set()
@@ -268,6 +308,7 @@ def __init__(
         self._descent_level = 0
         self.annotation_handlers = self.load_handlers()
         self.info = self.load_server()
+        self.filehandle = filehandle
 
     def skip_descent(self):
         return self.descent != "recursive" and self._descent_level > 0
@@ -375,13 +416,13 @@ def handle(self, data: Data) -> URIRef:
 
     def emit(self, triple: Triple):
         if self.formatter.streaming:
-            print(self.formatter.serialize_triple(triple))
+            print(self.formatter.serialize_triple(triple), file=self.filehandle)
         else:
             self.formatter.add(triple)
 
     def close(self):
         if not self.formatter.streaming:
-            print(self.formatter.serialize_graph())
+            print(self.formatter.serialize_graph(), file=self.filehandle)
 
     def rdf(
         self,
@@ -527,6 +568,12 @@ def _configure(self, parser: Parser) -> None:
             default=False,
             help="Remove leading and trailing whitespace from literals",
         )
+        parser.add_argument(
+            "--file",
+            type=str,
+            default=None,
+            help="Write RDF triples to the specified file",
+        )
         parser.set_defaults(func=self.action)
 
     @gateway_required
@@ -538,16 +585,18 @@ def action(self, args: Namespace) -> None:
         else:
             args.format = format_mapping()[args.format]
 
-        handler = Handler(
-            self.gateway,
-            formatter=args.format,
-            use_ellide=args.ellide,
-            trim_whitespace=args.trim_whitespace,
-            first_handler_wins=args.first_handler_wins,
-            descent=args.descent,
-        )
-        self.descend(self.gateway, args.target, handler)
-        handler.close()
+        with open_with_default(args.file) as fh:
+            handler = Handler(
+                self.gateway,
+                formatter=args.format,
+                use_ellide=args.ellide,
+                trim_whitespace=args.trim_whitespace,
+                first_handler_wins=args.first_handler_wins,
+                descent=args.descent,
+                filehandle=fh,
+            )
+            self.descend(self.gateway, args.target, handler)
+            handler.close()
 
     # TODO: move to handler?
     def descend(