New JSON-LD context-based version

omero_marshal/__init__.py

@@ -38,6 +38,7 @@ def get_encoder(t):
 
 
 def get_decoder(t):
+    t = get_full_type(t)
     try:
         return DECODERS[t]
     except KeyError:
@@ -77,6 +78,15 @@ def get_schema_version(version):
 SPW_SCHEMA_URL = '%s/%s/%s' % (BASE_URL, SPW_NS, SCHEMA_VERSION)
 
 
+def get_full_type(t):
+    if t.startswith("http"):
+        return t
+    elif t.startswith("omero:"):
+        return '%s/OMERO/%s#%s' % (BASE_URL, SCHEMA_VERSION, t[6:])
+    else:
+        return '%s/OME/%s#%s' % (BASE_URL, SCHEMA_VERSION, t)
+
+
 class MarshallingCtx(object):
 
     def __init__(self, encoders, decoders):
@@ -91,6 +101,7 @@ def get_encoder(self, t):
             return None
 
     def get_decoder(self, t):
+        t = get_full_type(t)
         try:
             return self.decoders[t]
         except KeyError:

omero_marshal/decode/__init__.py

@@ -30,6 +30,8 @@ def to_unit(self, v):
         if v is None:
             return None
         unit = v['@type'][v['@type'].rfind('#') + 1:]
+        if unit.startswith("omero:"):
+            unit = unit[6:]
         unit = getattr(omero.model, unit)
         return unit(
             float(v['Value']),

omero_marshal/decode/decoders/acquisitionmode.py

@@ -15,7 +15,7 @@
 
 class AcquisitionModeDecoder(EnumDecoder):
 
-    TYPE = 'TBD#AcquisitionMode'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2016-06#AcquisitionMode'
 
     OMERO_CLASS = AcquisitionModeI
 

omero_marshal/decode/decoders/checksum_algorithm.py

@@ -15,7 +15,8 @@
 
 class ChecksumAlgorithmDecoder(EnumDecoder):
 
-    TYPE = 'TBD#ChecksumAlgorithm'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#' \
+        'ChecksumAlgorithm'
 
     OMERO_CLASS = ChecksumAlgorithmI
 

omero_marshal/decode/decoders/contrastmethod.py

@@ -15,7 +15,7 @@
 
 class ContrastMethodDecoder(EnumDecoder):
 
-    TYPE = 'TBD#ContrastMethod'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2016-06#ContrastMethod'
 
     OMERO_CLASS = ContrastMethodI
 

omero_marshal/decode/decoders/details.py

@@ -15,7 +15,7 @@
 
 class DetailsDecoder(Decoder):
 
-    TYPE = 'TBD#Details'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#Details'
 
     OMERO_CLASS = DetailsI
 

omero_marshal/decode/decoders/dimensionorder.py

@@ -15,7 +15,7 @@
 
 class DimensionOrderDecoder(EnumDecoder):
 
-    TYPE = 'TBD#DimensionOrder'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2016-06#DimensionOrder'
 
     OMERO_CLASS = DimensionOrderI
 

omero_marshal/decode/decoders/externalinfo.py

@@ -15,7 +15,7 @@
 
 class ExternalInfoDecoder(Decoder):
 
-    TYPE = 'TBD#ExternalInfo'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#ExternalInfo'
 
     OMERO_CLASS = ExternalInfoI
 

omero_marshal/decode/decoders/format.py

@@ -15,7 +15,7 @@
 
 class FormatDecoder(EnumDecoder):
 
-    TYPE = 'TBD#Format'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#Format'
 
     OMERO_CLASS = FormatI
 

omero_marshal/decode/decoders/illumination.py

@@ -15,7 +15,7 @@
 
 class IlluminationDecoder(EnumDecoder):
 
-    TYPE = 'TBD#Illumination'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2016-06#IlluminationType'
 
     OMERO_CLASS = IlluminationI
 

omero_marshal/decode/decoders/original_file.py

@@ -15,7 +15,7 @@
 
 class OriginalFileDecoder(Decoder):
 
-    TYPE = 'TBD#OriginalFile'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#OriginalFile'
 
     OMERO_CLASS = OriginalFileI
 

omero_marshal/decode/decoders/permissions.py

@@ -15,7 +15,7 @@
 
 class PermissionsDecoder(Decoder):
 
-    TYPE = 'TBD#Permissions'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#Permissions'
 
     OMERO_CLASS = PermissionsI
 

omero_marshal/decode/decoders/photometricinterpretation.py

@@ -15,7 +15,8 @@
 
 class PhotometricInterpretationDecoder(EnumDecoder):
 
-    TYPE = 'TBD#PhotometricInterpretation'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#' \
+        'PhotometricInterpretation'
 
     OMERO_CLASS = PhotometricInterpretationI
 

omero_marshal/decode/decoders/pixelstype.py

@@ -15,7 +15,7 @@
 
 class PixelsTypeDecoder(EnumDecoder):
 
-    TYPE = 'TBD#PixelsType'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2016-06#PixelType'
 
     OMERO_CLASS = PixelsTypeI
 

omero_marshal/encode/__init__.py

@@ -9,14 +9,17 @@
 # jason@glencoesoftware.com.
 #
 
-
 # Needed to avoid import errors when this is the first import
 import omero.all  # noqa
 from omero import RType
 from omero_model_UnitBase import UnitBase
 from omero.rtypes import unwrap
 
 
+BASE_CONTEXT = "http://www.openmicroscopy.org/Schemas/OME/2016-06#"
+OMERO_CONTEXT = "http://www.openmicroscopy.org/Schemas/OMERO/2016-06#"
+
+
 class Encoder(object):
 
     TYPE = ''
@@ -35,22 +38,39 @@ def set_if_not_none(self, v, key, value):
             v[key] = value
 
     def encode_unit(self, v, key, value):
-        v[key] = {
-            '@type': 'TBD#%s' % value.__class__.__name__,
-            'Unit': value.getUnit().name,
-            'Symbol': value.getSymbol(),
-            'Value': value.getValue()
-        }
-
-    def encode(self, obj):
-        v = {'@type': self.TYPE}
+        k = value.__class__.__name__
+        if k in ("LengthI", "TimeI"):
+            v[key] = {
+                '@type': 'omero:%s' % k,
+                'Unit': value.getUnit().name,
+                'Symbol': value.getSymbol(),
+                'Value': value.getValue()
+            }
+        else:
+            raise Exception("unhandled unit: %s" % k)
+
+    def encode(self, obj, include_context=None):
+
+        if self.TYPE.startswith(BASE_CONTEXT):
+            v = {'@type': self.TYPE.split('#')[-1]}
+        elif self.TYPE.startswith(OMERO_CONTEXT):
+            v = {'@type': "omero:" + self.TYPE.split('#')[-1]}
+        else:
+            raise Exception("unknown prefix: %s" % self.TYPE)
+
+        if include_context is None or include_context:
+            v['@context'] = {
+                "@vocab": BASE_CONTEXT,
+                "omero": OMERO_CONTEXT,
+            }
+
         if hasattr(obj, 'id'):
             obj_id = unwrap(obj.id)
             if obj_id is not None:
                 v['@id'] = obj_id
         if hasattr(obj, 'details') and obj.details is not None:
             encoder = self.ctx.get_encoder(obj.details.__class__)
-            v['omero:details'] = encoder.encode(obj.details)
+            v['omero:details'] = encoder.encode(obj.details, False)
 
         return v
 

omero_marshal/encode/encoders/acquisitionmode.py

@@ -15,7 +15,7 @@
 
 class AcquisitionModeEncoder(EnumEncoder):
 
-    TYPE = 'TBD#AcquisitionMode'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2016-06#AcquisitionMode'
 
 
 encoder = (AcquisitionModeI, AcquisitionModeEncoder)

omero_marshal/encode/encoders/affinetransform.py

@@ -24,8 +24,9 @@ class AffineTransform201501Encoder(Encoder):
 
     TYPE = 'http://www.openmicroscopy.org/Schemas/ROI/2015-01#AffineTransform'
 
-    def encode(self, obj):
-        v = super(AffineTransform201501Encoder, self).encode(obj)
+    def encode(self, obj, include_context=None):
+        v = super(AffineTransform201501Encoder, self).encode(
+                obj, include_context)
         self.set_if_not_none(v, 'A00', obj.getA00())
         self.set_if_not_none(v, 'A10', obj.getA10())
         self.set_if_not_none(v, 'A01', obj.getA01())

omero_marshal/encode/encoders/annotation.py

@@ -47,8 +47,8 @@ class Annotation201501Encoder(Encoder):
 
     TYPE = 'http://www.openmicroscopy.org/Schemas/SA/2015-01#Annotation'
 
-    def encode(self, obj):
-        v = super(Annotation201501Encoder, self).encode(obj)
+    def encode(self, obj, include_context=None):
+        v = super(Annotation201501Encoder, self).encode(obj, include_context)
         self.set_if_not_none(v, 'Description', obj.description)
         self.set_if_not_none(v, 'Namespace', obj.ns)
         return v
@@ -63,15 +63,15 @@ class Annotatable201501Encoder(Encoder):
 
     TYPE = 'http://www.openmicroscopy.org/Schemas/SA/2015-01#AnnotationRef'
 
-    def encode(self, obj):
-        v = super(Annotatable201501Encoder, self).encode(obj)
+    def encode(self, obj, include_context=None):
+        v = super(Annotatable201501Encoder, self).encode(obj, include_context)
         if obj.isAnnotationLinksLoaded() and obj.sizeOfAnnotationLinks() > 0:
             annotations = list()
             for annotation_link in obj.copyAnnotationLinks():
                 annotation = annotation_link.child
                 annotation_encoder = self.ctx.get_encoder(annotation.__class__)
                 annotations.append(
-                    annotation_encoder.encode(annotation)
+                    annotation_encoder.encode(annotation, False)
                 )
             v['Annotations'] = annotations
         return v

omero_marshal/encode/encoders/boolean_annotation.py

@@ -19,8 +19,9 @@ class BooleanAnnotation201501Encoder(AnnotationEncoder):
     TYPE = 'http://www.openmicroscopy.org/Schemas/SA/2015-01' \
         '#BooleanAnnotation'
 
-    def encode(self, obj):
-        v = super(BooleanAnnotation201501Encoder, self).encode(obj)
+    def encode(self, obj, include_context=None):
+        v = super(BooleanAnnotation201501Encoder, self).encode(
+                obj, include_context)
         self.set_if_not_none(v, 'Value', obj.boolValue)
         return v
 

omero_marshal/encode/encoders/channel.py

@@ -18,8 +18,8 @@ class Channel201501Encoder(AnnotatableEncoder):
 
     TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2015-01#Channel'
 
-    def encode(self, obj):
-        v = super(Channel201501Encoder, self).encode(obj)
+    def encode(self, obj, include_context=None):
+        v = super(Channel201501Encoder, self).encode(obj, include_context)
         color = self.rgba_to_int(obj.red, obj.green, obj.blue, obj.alpha)
         self.set_if_not_none(v, 'Color', color)
         self.set_if_not_none(v, 'omero:lookupTable', obj.lookupTable)
@@ -49,19 +49,19 @@ def encode(self, obj):
                 contrast_method_encoder = \
                     self.ctx.get_encoder(contrast_method.__class__)
                 v['ContrastMethod'] = \
-                    contrast_method_encoder.encode(contrast_method)
+                    contrast_method_encoder.encode(contrast_method, False)
             illumination = logical_channel.illumination
             if illumination is not None and illumination.isLoaded():
                 illumination_encoder = \
                     self.ctx.get_encoder(illumination.__class__)
                 v['Illumination'] = \
-                    illumination_encoder.encode(illumination)
+                    illumination_encoder.encode(illumination, False)
             acquisition_mode = logical_channel.mode
             if acquisition_mode is not None and acquisition_mode.isLoaded():
                 acquisition_mode_encoder = \
                     self.ctx.get_encoder(acquisition_mode.__class__)
                 v['AcquisitionMode'] = \
-                    acquisition_mode_encoder.encode(acquisition_mode)
+                    acquisition_mode_encoder.encode(acquisition_mode, False)
             photometric_interpretation = \
                 logical_channel.photometricInterpretation
             if photometric_interpretation is not None \
@@ -70,7 +70,7 @@ def encode(self, obj):
                     self.ctx.get_encoder(photometric_interpretation.__class__)
                 v['omero:photometricInterpretation'] = \
                     photometric_interpretation_encoder.encode(
-                        photometric_interpretation
+                        photometric_interpretation, False
                     )
         return v
 

omero_marshal/encode/encoders/checksum_algorithm.py

@@ -15,7 +15,8 @@
 
 class ChecksumAlgorithmEncoder(EnumEncoder):
 
-    TYPE = 'TBD#ChecksumAlgorithm'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OMERO/2016-06#' \
+        'ChecksumAlgorithm'
 
 
 encoder = (ChecksumAlgorithmI, ChecksumAlgorithmEncoder)

omero_marshal/encode/encoders/comment_annotation.py

@@ -19,8 +19,9 @@ class CommentAnnotation201501Encoder(TextAnnotationEncoder):
     TYPE = 'http://www.openmicroscopy.org/Schemas/SA/2015-01' \
         '#CommentAnnotation'
 
-    def encode(self, obj):
-        v = super(CommentAnnotation201501Encoder, self).encode(obj)
+    def encode(self, obj, include_context=None):
+        v = super(CommentAnnotation201501Encoder, self).encode(
+                obj, include_context)
         return v
 
 

omero_marshal/encode/encoders/contrastmethod.py

@@ -15,7 +15,7 @@
 
 class ContrastMethodEncoder(EnumEncoder):
 
-    TYPE = 'TBD#ContrastMethod'
+    TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2016-06#ContrastMethod'
 
 
 encoder = (ContrastMethodI, ContrastMethodEncoder)

omero_marshal/encode/encoders/dataset.py

@@ -18,8 +18,8 @@ class Dataset201501Encoder(AnnotatableEncoder):
 
     TYPE = 'http://www.openmicroscopy.org/Schemas/OME/2015-01#Dataset'
 
-    def encode(self, obj):
-        v = super(Dataset201501Encoder, self).encode(obj)
+    def encode(self, obj, include_context=None):
+        v = super(Dataset201501Encoder, self).encode(obj, include_context)
         self.set_if_not_none(v, 'Name', obj.name)
         self.set_if_not_none(v, 'Description', obj.description)
         if obj.isImageLinksLoaded() and obj.sizeOfImageLinks() > 0:
@@ -28,7 +28,7 @@ def encode(self, obj):
                 image = image_link.child
                 image_encoder = self.ctx.get_encoder(image.__class__)
                 images.append(
-                    image_encoder.encode(image)
+                    image_encoder.encode(image, False)
                 )
             v['Images'] = images
         return v