extra metadata dict, initialized inside from_owl_uri

cdci_data_analysis/analysis/parameters.py

@@ -210,6 +210,8 @@
                  allowed_values=None,
                  min_value = None,
                  max_value = None,
+
+                 extra_metadata=None,
                  **kwargs
                  ):
 
@@ -261,6 +263,7 @@
         self._max_value = max_value
         self._bound_units = self.units
         self.value = value
+        self.extra_metadata = extra_metadata
 
 
         self._arg_list = [self.name]
@@ -463,6 +466,8 @@
             restrictions['schema'] = self.schema
         if restrictions:
             reprjson[0]['restrictions'] = restrictions
+        if getattr(self, 'extra_metadata', None) is not None:
+            reprjson[0]['extra_metadata'] = self.extra_metadata
         if getattr(self, 'owl_uris', None):
             if isinstance(self.owl_uris, str):
                 reprjson[0]['owl_uri'] = [ self.owl_uris ]
@@ -487,14 +492,16 @@
                      **kwargs):
         from oda_api.ontology_helper import Ontology
 
+        metadata_keys = ['label', 'description', 'group']
+
         if ontology_path is not None and ontology_object is not None:
             raise RuntimeError("Both ontology_path and ontology_object parameters are set.")
         elif ontology_path is None and ontology_object is None:
             logger.warning('Ontology path/object not set in Parameter.from_owl_uri(). '
                 'Trying to find parameter which have %s directly set. '
                 'extra_ttl will be ignored ', owl_uri)
             parameter_hierarchy = [ owl_uri ]
-            par_format = par_unit = allowed_values = min_value = max_value = None
+            par_format = par_unit = allowed_values = min_value = max_value = label = description = group = None
         else:
             if ontology_path is not None:
                 if isinstance(ontology_path, (str, os.PathLike)):
@@ -514,13 +521,18 @@
             par_unit = onto.get_parameter_unit(owl_uri)
             min_value, max_value = onto.get_limits(owl_uri)
             allowed_values = onto.get_allowed_values(owl_uri)
-
+            label = onto.get_direct_annotation(owl_uri, "label")
+            description = onto.get_direct_annotation(owl_uri, "description")
+            group = onto.get_direct_annotation(owl_uri, "group")
+
         for owl_superclass_uri in parameter_hierarchy:
             for python_subclass in subclasses_recursive(cls):
                 logger.debug("searching for class with owl_uri=%s, found %s", owl_superclass_uri, python_subclass)
                 if python_subclass.matches_owl_uri(owl_superclass_uri):
                     logger.info("will construct %s by owl_uri %s", python_subclass, owl_superclass_uri)
-                    call_kwargs = {}
+                    call_kwargs = {
+                        'extra_metadata': {key: val for key, val in zip(metadata_keys, [label, description, group]) if
+                                           val is not None}}
                     call_signature = signature(python_subclass)
                     var_kw_signature = call_parameter.VAR_KEYWORD in [x.kind for x in call_signature.parameters.values()]
 
@@ -566,15 +578,16 @@
 class String(Parameter):
     owl_uris = ("http://www.w3.org/2001/XMLSchema#str", "http://odahub.io/ontology#String")
 
-    def __init__(self, value=None, name_format='str', name=None, allowed_values = None):
+    def __init__(self, value=None, name_format='str', name=None, allowed_values = None, extra_metadata = None):
 
         _allowed_units = ['str']
         super().__init__(value=value,
                          units=name_format,
                          check_value=self.check_name_value,
                          name=name,
                          allowed_units=_allowed_units,
-                         allowed_values=allowed_values)
+                         allowed_values=allowed_values,
+                         extra_metadata=extra_metadata)
 
     @staticmethod
     def check_name_value(value, units=None, name=None, par_format=None):
@@ -671,7 +684,8 @@
                  check_value=None, 
                  min_value= None,
                  max_value = None,
-                 units_name = None):
+                 units_name = None,
+                 extra_metadata=None):
 
         super().__init__(value=value,
                          units=units,
@@ -684,7 +698,8 @@
                          allowed_units=allowed_units,
                          min_value=min_value,
                          max_value=max_value,
-                         units_name = units_name)
+                         units_name = units_name,
+                         extra_metadata=extra_metadata)
 
 
 
@@ -700,7 +715,8 @@
                  max_value = None,
                  units_name = None,
                  default_units = None,
-                 allowed_units = None):
+                 allowed_units = None,
+                 extra_metadata=None):
 
         super().__init__(value=value,
                          units=units,
@@ -712,7 +728,8 @@
                          allowed_units=allowed_units,
                          min_value = min_value,
                          max_value = max_value,
-                         units_name = units_name)
+                         units_name = units_name,
+                         extra_metadata=extra_metadata)
 
     def set_par_internal_value(self, value):
         if isinstance(value, float):
@@ -725,13 +742,14 @@
     owl_uris = ("http://odahub.io/ontology#TimeInstant",)
     format_kw = 'T_format'
 
-    def __init__(self, value=None, T_format='isot', name=None, Time_format_name='T_format', par_default_format='isot'):
+    def __init__(self, value=None, T_format='isot', name=None, Time_format_name='T_format', par_default_format='isot', extra_metadata=None):
 
         super().__init__(value=value,
                          par_format=T_format,
                          par_format_name=Time_format_name,
                          par_default_format=par_default_format,
-                         name=name)
+                         name=name,
+                         extra_metadata=extra_metadata)
 
     def get_default_value(self):
         return self.get_value_in_default_format()
@@ -776,15 +794,16 @@
     owl_uris = ("http://odahub.io/ontology#TimeDeltaIsDeprecated",) 
     format_kw = 'delta_T_format'
 
-    def __init__(self, value=None, delta_T_format='sec', name=None, delta_T_format_name=None, par_default_format='sec'):
+    def __init__(self, value=None, delta_T_format='sec', name=None, delta_T_format_name=None, par_default_format='sec', extra_metadata=None):
         logging.warning(('TimeDelta parameter is deprecated. '
                          'It derives from Time, which is confusing. '
                          'Consider using TimeInterval parameter.'))
         super().__init__(value=value,
                          T_format=delta_T_format,
                          Time_format_name=delta_T_format_name,
                          par_default_format=par_default_format,
-                         name=name)
+                         name=name,
+                         extra_metadata=extra_metadata)
 
     def get_value_in_format(self, units):
         return getattr(self._astropy_time_delta, units)
@@ -816,7 +835,8 @@
                  default_units='s', 
                  min_value=None, 
                  max_value=None,
-                 units_name = None):
+                 units_name = None,
+                 extra_metadata=None):
 
         _allowed_units = ['s', 'minute', 'hour', 'day', 'year']
         super().__init__(value=value,
@@ -826,13 +846,14 @@
                          min_value=min_value,
                          max_value=max_value,
                          units_name = units_name,
-                         allowed_units=_allowed_units)
+                         allowed_units=_allowed_units,
+                         extra_metadata=extra_metadata)
 
 class InputProdList(Parameter):
     owl_uris = ('http://odahub.io/ontology#InputProdList',)
 
     # TODO removal of the leading underscore cannot be done for compatibility with the plugins
-    def __init__(self, value=None, _format='names_list', name: str = None):
+    def __init__(self, value=None, _format='names_list', name: str = None, extra_metadata=None):
         _allowed_units = ['names_list']
 
         if value is None:
@@ -842,7 +863,8 @@
                          par_format=_format,
                          check_value=self.check_list_value,
                          name=name,
-                         allowed_units=_allowed_units)
+                         allowed_units=_allowed_units,
+                         extra_metadata=extra_metadata)
 
     @staticmethod
     def _split(str_list):
@@ -903,7 +925,8 @@
                  name=None, 
                  min_value = None, 
                  max_value = None,
-                 units_name = None):
+                 units_name = None,
+                 extra_metadata=None):
 
         super().__init__(value=value,
                          units=units,
@@ -913,7 +936,8 @@
                          allowed_units=None,
                          min_value = min_value,
                          max_value = max_value,
-                         units_name = units_name)
+                         units_name = units_name,
+                         extra_metadata=extra_metadata)
 
 
 class Energy(Float):
@@ -928,7 +952,8 @@
                  check_value=None, 
                  min_value = None, 
                  max_value = None,
-                 units_name = None):
+                 units_name = None,
+                 extra_metadata=None):
 
         _allowed_units = ['keV', 'eV', 'MeV', 'GeV', 'TeV', 'Hz', 'MHz', 'GHz']
 
@@ -940,7 +965,8 @@
                          allowed_units=_allowed_units,
                          min_value = min_value,
                          max_value = max_value,
-                         units_name = units_name)
+                         units_name = units_name,
+                         extra_metadata=extra_metadata)
 
 class SpectralBoundary(Energy):
     def __init__(self, 
@@ -951,7 +977,8 @@
                  check_value=None, 
                  min_value=None, 
                  max_value=None, 
-                 units_name=None):
+                 units_name=None,
+                 extra_metadata=None):
 
         # retro-compatibility with integral plugin
         if check_value is None:
@@ -964,7 +991,8 @@
                          check_value=check_value, 
                          min_value=min_value, 
                          max_value=max_value, 
-                         units_name=units_name)
+                         units_name=units_name,
+                         extra_metadata=extra_metadata)
 
     @staticmethod
     def check_energy_value(value, units, name): 
@@ -973,7 +1001,7 @@
 
 class DetectionThreshold(Float):
     owl_uris = ("http://odahub.io/ontology#DetectionThreshold",)    
-    def __init__(self, value=None, units='sigma', name=None, min_value = None, max_value = None):
+    def __init__(self, value=None, units='sigma', name=None, min_value = None, max_value = None, extra_metadata=None):
         _allowed_units = ['sigma']
 
         super().__init__(value=value,
@@ -982,7 +1010,8 @@
                          name=name,
                          allowed_units=_allowed_units,
                          min_value = min_value,
-                         max_value = max_value)
+                         max_value = max_value,
+                         extra_metadata=extra_metadata)
 
     # 'sigma' is not astropy unit, so need to override methods
     def get_value_in_units(self, units):
@@ -995,24 +1024,26 @@
             self._value = None
 
 class UserCatalog(Parameter):
-    def __init__(self, value=None, name_format='str', name=None):
+    def __init__(self, value=None, name_format='str', name=None, extra_metadata=None):
         _allowed_units = ['str']
         super().__init__(value=value,
                          par_format=name_format,
                          check_value=None,
                          name=name,
-                         allowed_units=_allowed_units)
+                         allowed_units=_allowed_units,
+                         extra_metadata=extra_metadata)
 
 class Boolean(Parameter):
     owl_uris = ('http://www.w3.org/2001/XMLSchema#bool',"http://odahub.io/ontology#Boolean")
 
-    def __init__(self, value=None, name=None):
+    def __init__(self, value=None, name=None, extra_metadata=None):
 
         self._true_rep = ['True', 'true', 'yes', '1', True]
         self._false_rep = ['False', 'false', 'no', '0', False]
         super().__init__(value=value,
                          name=name,
-                         allowed_values=self._true_rep+self._false_rep
+                         allowed_values=self._true_rep+self._false_rep,
+                         extra_metadata = extra_metadata
                          )
 
     @property
@@ -1031,15 +1062,16 @@
 class StructuredParameter(Parameter):
     owl_uris = ("http://odahub.io/ontology#StructuredParameter")
 
-    def __init__(self, value=None, name=None, schema={"oneOf": [{"type": "object"}, {"type": "array"}]}):
+    def __init__(self, value=None, name=None, schema={"oneOf": [{"type": "object"}, {"type": "array"}]}, extra_metadata=None):
 
         self.schema = schema
 
         if self.schema is None:
             logger.warning("Parameter %s: Schema is not defined, will allow any structure.", name)
 
         super().__init__(value=value,
-                         name=name)
+                         name=name,
+                         extra_metadata=extra_metadata)
 
     def check_schema(self):
         if self.schema is not None:
@@ -1065,7 +1097,7 @@
 class PhosphorosFiltersTable(StructuredParameter):
     owl_uris = ('http://odahub.io/ontology#PhosphorosFiltersTable')
 
-    def __init__(self, value=None, name=None):
+    def __init__(self, value=None, name=None, extra_metadata=None):
 
         # TODO: either list or the whole schema may be loaded from the external file, purely based on URI.
         #       If there is no additional check, this would allow to avoid even having the class.
@@ -1102,7 +1134,7 @@
                   "required": ["filter", "flux", "flux_error"]
                   }
 
-        super().__init__(value=value, name=name, schema=schema)
+        super().__init__(value=value, name=name, schema=schema, extra_metadata=extra_metadata)
 
     def additional_check(self):
         assert len(self._value['filter']) == len(self._value['flux']) == len(self._value['flux_error'])

tests/test_parameters.py

@@ -1,4 +1,5 @@
 import pytest
+import os
 
 from cdci_data_analysis.analysis.instrument import Instrument
 from cdci_data_analysis.analysis.queries import (
@@ -422,7 +423,7 @@ def test_boolean_parameter(inval, iswrong, expected):
     True, 100, Energy),
     ])
 def test_parameter_class_from_owl_uri(uri, extra_ttl, use_ontology, value, param_type):
-    ontology_path = 'tests/oda-ontology.ttl' if use_ontology else None
+    ontology_path = os.path.join(os.path.dirname(__file__), 'oda-ontology.ttl') if use_ontology else None
     param = Parameter.from_owl_uri(uri, 
                                    value=value,
                                    extra_ttl = extra_ttl,