Merge pull request #43 from joshmoore/fix-42-rois

Author: joshmoore

.pre-commit-config.yaml

@@ -34,14 +34,14 @@ repos:
           - --autofix
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 7.2.0
     hooks:
       - id: flake8
         additional_dependencies: [
           flake8-blind-except,
           flake8-builtins,
           flake8-rst-docstrings,
-          flake8-logging-format,
+          # flake8-logging-format,
         ]
         args: [
           # default black line length is 88

src/omero_rdf/__init__.py

@@ -394,7 +394,6 @@ def handle(self, data: Data) -> URIRef:
         Returns the id for the data object itself
         """
         # TODO: Add quad representation as an option
-        output: Triple
 
         str_id = data.get("@id")
         if not str_id:
@@ -674,15 +673,18 @@ def descend(
         elif isinstance(target, Image):
             img = self._lookup(gateway, "Image", target.id)
             imgid = handler(img)
-            pixid = handler(img.getPrimaryPixels())
-            handler.emit((pixid, DCTERMS.isPartOf, imgid))
-            handler.emit((imgid, DCTERMS.hasPart, pixid))
+            if img.getPrimaryPixels() is not None:
+                pixid = handler(img.getPrimaryPixels())
+                handler.emit((pixid, DCTERMS.isPartOf, imgid))
+                handler.emit((imgid, DCTERMS.hasPart, pixid))
             for annotation in img.listAnnotations(None):
                 img._loadAnnotationLinks()
                 annid = handler(annotation)
                 handler.emit((annid, DCTERMS.isPartOf, imgid))
             for roi in self._get_rois(gateway, img):
-                handler(roi)
+                roiid = handler(roi)
+                handler.emit((roiid, DCTERMS.isPartOf, pixid))
+                handler.emit((pixid, DCTERMS.hasPart, roiid))
             return imgid
 
         else:

test/integration/clitest/test_rdf.py

@@ -21,6 +21,10 @@
 
 from omero.testlib.cli import CLITest
 from omero_rdf import RdfControl
+from omero.model import RoiI
+
+from rdflib import Graph, Namespace, RDF
+from rdflib.namespace import DCTERMS
 
 
 class TestRdf(CLITest):
@@ -41,3 +45,34 @@ def test_rdf(self, capfd):
         self.args += [obj_arg]
         out = self.rdf(capfd)
         assert out
+
+    def test_rois(self, capfd):
+
+        update = self.client.sf.getUpdateService()
+
+        # Setup a test image with a roi
+        pix = self.create_pixels()
+        img = pix.image
+        roi = RoiI()
+        img.addRoi(roi)
+        img = update.saveAndReturnObject(img)
+
+        # Export the test image
+        object_type = "Image"
+        obj_arg = f"{object_type}:{img.id.val}"
+        self.args += ["-Fturtle", obj_arg]
+        out = self.rdf(capfd)
+
+        # Check that it contains the roi linked to the image (issue#42)
+        g = Graph()
+        g.parse(data=out, format="ttl")
+
+        xml = Namespace("http://www.openmicroscopy.org/Schemas/OME/2016-06#")
+
+        found = False
+        for s, p, o in g.triples((None, DCTERMS.isPartOf, None)):
+            print(s, p, o)
+            if (s, RDF.type, xml.ROI) in g and (o, RDF.type, xml.Pixels) in g:
+                found = True
+
+        assert found, "no link between pixels and ROI:" + g.serialize()