Merge pull request #332 from mpsonntag/rdfsubclasses

RDF converter: subclassing file fix

Author: jgrewe

CHANGELOG.md

@@ -5,6 +5,9 @@ until the next release.
 
 # Latest changes in master
 
+## Minor changes, updates and fixes
+- The `section_subclasses.yaml` file is moved from the `doc` folder to the new `odml/resources` folder. This allows usage of the file with all install options. See issue #212 for details.
+
 # Version 1.4.3
 
 ## Introduction of odML templates support and update in odML terminology handling

MANIFEST.in

@@ -1,4 +1,4 @@
 include LICENSE
 include README.rst
 include odml/info.json
-include doc/section_subclasses.yaml
+include odml/resources/section_subclasses.yaml

docs/index.md

@@ -135,7 +135,8 @@ its identifier RRID:SCR_001376 and/or the reference:
 
 ### Referenced By
 
-- Dragly et al (2018) [doi:10.3389/fninf.2018.000169](https://doi.org/10.3389/fninf.2018.000169)
+- Sprenger et al (2019) [doi:10.3389/fninf.2019.00062](https://doi.org/10.3389/fninf.2019.00062)
+- Dragly et al (2018) [doi:10.3389/fninf.2018.00016](https://doi.org/10.3389/fninf.2018.00016)
 - Brochier et al (2018) [doi:10.1038/sdata.2018.55](https://doi.org/10.1038/sdata.2018.55)
 - Moucek et al (2017) [doi:10.1038/sdata.2016.121](https://doi.org/10.1038/sdata.2016.121)
 - Papez et al (2017) [doi:10.3389/fninf.2017.00024](https://doi.org/10.3389/fninf.2017.00024)

doc/section_subclasses.yaml renamed to odml/resources/section_subclasses.yaml

@@ -2,7 +2,27 @@ analysis: Analysis
 analysis/psth: PSTH
 analysis/power_spectrum: PowerSpectrum
 cell: Cell
+datacite/alternate_identifier: AlternateIdentifier
+datacite/contributor: Contributer
+datacite/contributor/affiliation: Affiliation
+datacite/contributor/named_identifier: NamedIdentifier
+datacite/creator: Creator
+datacite/creator/affiliation: Affiliation
+datacite/creator/named_identifier: NamedIdentifier
+datacite/date: Date
+datacite/description: Description
+datacite/format: Format
+datacite/funding_reference: FundingReference
+datacite/geo_location: GeoLocation
+datacite/identifier: Identifier
+datacite/related_identifier: RelatedIdentifier
+datacite/resource_type: ResourceType
+datacite/rights: Rights
+datacite/size: Size
+datacite/subject: Subject
+datacite/title: Title
 dataset: Dataset
+data_reference: DataReference
 blackrock: Blackrock
 electrode: Electrode
 event: Event
@@ -51,4 +71,4 @@ stimulus/sine_wave: Sinewave
 stimulus/square_wave: Squarewave
 stimulus/white_noise: Whitenoise
 subject: Subject
-carmen_mini: CarmenMini
+carmen_mini: CarmenMini

odml/tools/rdf_converter.py

@@ -43,8 +43,8 @@ def __init__(self, odml_documents):
 
         self.section_subclasses = {}
 
-        subclass_path = os.path.join(dirname(dirname(dirname(abspath(__file__)))),
-                         'doc', 'section_subclasses.yaml')
+        subclass_path = os.path.join(odml.__path__[0], 'resources',
+                                     'section_subclasses.yaml')
 
         if os.path.isfile(subclass_path):
             with open(subclass_path, "r") as f:
@@ -53,6 +53,8 @@ def __init__(self, odml_documents):
                 except yaml.parser.ParserError as err:
                     print(err)
                     return
+        else:
+            print("[Warning] Could not find subclass file '%s'" % subclass_path)
 
     def convert_to_rdf(self):
         self.hub_root = URIRef(odmlns.Hub)
@@ -125,8 +127,10 @@ def save_element(self, e, node=None):
                     self.g.add((curr_node, fmt.rdf_map(k), node))
                     self.save_element(p, node)
             elif isinstance(fmt, Property.__class__) and \
-                    k == 'value' and len(getattr(e, k)) > 0:
-                values = getattr(e, k)
+                    k == 'value' and len(getattr(e, fmt.map(k))) > 0:
+                # "value" needs to be mapped to its appropriate
+                # Property library attribute.
+                values = getattr(e, fmt.map(k))
                 seq = URIRef(odmlns + unicode(uuid.uuid4()))
                 self.g.add((seq, RDF.type, RDF.Seq))
                 self.g.add((curr_node, fmt.rdf_map(k), seq))

test/test_rdf_writer.py

@@ -132,7 +132,7 @@ def test_adding_values(self):
                                                object=Literal("val")))), 3)
 
     def test_section_subclass(self):
-        p = os.path.join(dirname(dirname(abspath(__file__))), 'doc', 'section_subclasses.yaml')
+        p = os.path.join(odml.__path__[0], 'resources', 'section_subclasses.yaml')
         with open(p, "r") as f:
             subclass = yaml.load(f)