sanitizing json2jsonld serialization and fixing failing tests resulting from alterations to isatools/model and isatools/database

Author: oerc0042

isatools/database/models/assay.py

@@ -57,6 +57,7 @@ class Assay(Base):
     def to_json(self):
         characteristic_categories = get_characteristic_categories(self.characteristic_categories)
         return {
+            "@id": str(self.assay_id),
             "filename": self.filename,
             "technologyPlatform": self.technology_platform,
             "measurementType": self.measurement_type.to_json(),

isatools/database/models/ontology_annotation.py

@@ -57,7 +57,7 @@ def to_json(self):
         return {
             "@id": self.ontology_annotation_id,
             "annotationValue": self.annotation_value,
-            "termSource": self.term_source_id if self.term_source_id else None,
+            "termSource": self.term_source.name if self.term_source else None,
             "termAccession": self.term_accession,
             "comments": [c.to_json() for c in self.comments],
         }

isatools/database/models/ontology_source.py

@@ -33,7 +33,7 @@ def to_json(self) -> dict:
         :return: The dictionary representation of the object taken from the database
         """
         return {
-            "id": self.ontology_source_id,
+            "@id": self.ontology_source_id,
             "name": self.name,
             "file": self.file,
             "version": self.version,
@@ -56,11 +56,11 @@ def to_sql(self, session) -> OntologySource:
 
         :return: The SQLAlchemy object ready to be committed to the database session.
         """
-        ontology_source = session.get(OntologySource, self.name)
+        ontology_source = session.get(OntologySource, self.id)
         if ontology_source:
             return ontology_source
         ontology_source = OntologySource(
-            ontology_source_id=self.name,
+            ontology_source_id=self.id,
             name=self.name,
             file=self.file,
             version=self.version,

isatools/database/models/study.py

@@ -75,6 +75,7 @@ def to_json(self) -> dict:
         """
         characteristics_categories = get_characteristic_categories(self.characteristic_categories)
         return {
+            "@id": str(self.study_id),
             "title": self.title,
             "filename": self.filename,
             "identifier": self.identifier,

isatools/model/assay.py

@@ -1,13 +1,14 @@
 from isatools.model.comments import Commentable
 from isatools.model.datafile import DataFile
+from isatools.model.identifiable import Identifiable
 from isatools.model.loader_indexes import loader_states as indexes
 from isatools.model.material import Material
 from isatools.model.mixins import StudyAssayMixin
 from isatools.model.ontology_annotation import OntologyAnnotation
 from isatools.model.process import Process
 
 
-class Assay(Commentable, StudyAssayMixin, object):
+class Assay(Commentable, Identifiable, StudyAssayMixin, object):
     """An Assay represents a test performed either on material taken from a
     subject or on a whole initial subject, producing qualitative or
     quantitative
@@ -38,6 +39,7 @@ class Assay(Commentable, StudyAssayMixin, object):
 
     def __init__(
         self,
+        id_="",
         measurement_type=None,
         technology_type=None,
         technology_platform="",
@@ -72,6 +74,7 @@ def __init__(
         self.__technology_platform = technology_platform
         self.data_files = data_files or []
 
+        self.id = id_
     @property
     def measurement_type(self):
         """:obj:`OntologyAnnotation: an ontology annotation representing the
@@ -200,6 +203,7 @@ def __ne__(self, other):
 
     def to_dict(self, ld=False):
         assay = {
+            "@id": self.id,
             "measurementType": self.measurement_type.to_dict(ld=ld) if self.measurement_type else "",
             "technologyType": self.technology_type.to_dict(ld=ld) if self.technology_type else "",
             "technologyPlatform": self.technology_platform,
@@ -217,6 +221,7 @@ def to_dict(self, ld=False):
         return self.update_isa_object(assay, ld)
 
     def from_dict(self, assay, isa_study):
+        self.id = assay.get("@id", "")
         self.technology_platform = assay.get("technologyPlatform", "")
         self.filename = assay.get("filename", "")
         self.load_comments(assay.get("comments", []))

isatools/model/mixins.py

@@ -18,16 +18,16 @@
 
 
 class MetadataMixin(metaclass=ABCMeta):
-    """Abstract mixin class to contain metadata fields found in Investigation
+    """ Abstract mixin class to contain metadata fields found in Investigation
     and Study sections of ISA
 
     Attributes:
-        identifier: An identifier associated with objects of this class.
-        title: A title associated with objects of this class.
-        description: A description associated with objects of this class.
-        submission_date: A submission date associated with objects of this
+    identifier: An identifier associated with objects of this class.
+    title: A title associated with objects of this class.
+    description: A description associated with objects of this class.
+    submission_date: A submission date associated with objects of this
             class.
-        public_release_date: A submission date associated with objects of this
+    public_release_date: A submission date associated with objects of this
             class.
     """
 
@@ -161,24 +161,23 @@ def contacts(self, val):
 
 
 class StudyAssayMixin(metaclass=ABCMeta):
-    """Abstract mixin class to contain common fields found in Study
+    """ Abstract mixin class to contain common fields found in Study
     and Assay sections of ISA
 
     Attributes:
-        filename: A field to specify the file for compatibility with ISA-Tab.
-        materials: Materials associated with the Study or Assay.
-        sources: Sources associated with the Study or Assay.
-        samples: Samples associated with the Study or Assay.
-        other_material: Other Material types associated with the Study or
-        Assay.
-        units: A list of Units used in the annotation of materials.
-        characteristic_categories-: A list of OntologyAnnotation used in
-            the annotation of material characteristics.
-        process_sequence: A list of Process objects representing the
-            experimental graphs.
-        comments: Comments associated with instances of this class.
-        graph: Graph representation of the experimental graph.
-
+    filename: A field to specify the file for compatibility with ISA-Tab.
+    materials: Materials associated with the Study or Assay.
+    sources: Sources associated with the Study or Assay.
+    samples: Samples associated with the Study or Assay.
+    other_material: Other Material types associated with the Study or
+    Assay.
+    units: A list of Units used in the annotation of materials.
+    characteristic_categories-: A list of OntologyAnnotation used in
+        the annotation of material characteristics.
+    process_sequence: A list of Process objects representing the
+        experimental graphs.
+    comments: Comments associated with instances of this class.
+    graph: Graph representation of the experimental graph.
     """
 
     def __init__(
@@ -252,7 +251,7 @@ def sources(self, val):
             raise AttributeError("{}.sources must be iterable containing Sources".format(type(self).__name__))
 
     def add_source(self, name="", characteristics=None, comments=None):
-        """Adds a new source to the source materials list.
+        """ Adds a new source to the source materials list.
         :param string name: Source name
         :param list[Characteristics] characteristics: Characteristics about the Source
         :param list comments: Comments about the Source
@@ -261,7 +260,7 @@ def add_source(self, name="", characteristics=None, comments=None):
         self.sources.append(s)
 
     def yield_sources(self, name=None):
-        """Gets an iterator of matching sources for a given name.
+        """ Gets an iterator of matching sources for a given name.
 
         Args:
             name: Source name
@@ -273,7 +272,7 @@ def yield_sources(self, name=None):
         return filter(lambda x: x, self.sources) if name is None else filter(lambda x: x.name == name, self.sources)
 
     def get_source(self, name):
-        """Gets the first matching source material for a given name.
+        """ Gets the first matching source material for a given name.
 
         Args:
             name: Source name
@@ -288,7 +287,7 @@ def get_source(self, name):
         return None
 
     def yield_sources_by_characteristic(self, characteristic=None):
-        """Gets an iterator of matching sources for a given characteristic.
+        """ Gets an iterator of matching sources for a given characteristic.
 
         Args:
             characteristic: Source characteristic
@@ -302,7 +301,7 @@ def yield_sources_by_characteristic(self, characteristic=None):
         return filter(lambda x: characteristic in x.characteristics, self.sources)
 
     def get_source_by_characteristic(self, characteristic):
-        """Gets the first matching source material for a given characteristic.
+        """ Gets the first matching source material for a given characteristic.
 
         Args:
             characteristic: Source characteristic
@@ -318,7 +317,7 @@ def get_source_by_characteristic(self, characteristic):
         return None
 
     def get_source_names(self):
-        """Gets all of the source names.
+        """ Gets all the source names.
 
         Returns:
             :obj:`list` of str.
@@ -340,7 +339,7 @@ def samples(self, val):
             raise AttributeError("{}.samples must be iterable containing Samples".format(type(self).__name__))
 
     def add_sample(self, name="", characteristics=None, factor_values=None, derives_from=None, comments=None):
-        """Adds a new sample to the sample materials list.
+        """ Adds a new sample to the sample materials list.
         :param string name: Sample name
         :param list[Characteristics] characteristics: Characteristics about the sample
         :param list comments: Comments about the sample
@@ -358,14 +357,14 @@ def add_sample(self, name="", characteristics=None, factor_values=None, derives_
         self.samples.append(sample)
 
     def yield_samples(self, name=None):
-        """Gets an iterator of matching samples for a given name.
+        """ Gets an iterator of matching samples for a given name.
         :param string name: Sample name
         :return: object:`filter` of object:`Source` that can be iterated on.  If name is None, yields all samples.
         """
         return filter(lambda x: x, self.samples) if name is None else filter(lambda x: x.name == name, self.samples)
 
     def get_sample(self, name):
-        """Gets the first matching sample material for a given name.
+        """ Gets the first matching sample material for a given name.
 
         Args:
             name: Sample name
@@ -380,7 +379,7 @@ def get_sample(self, name):
         return None
 
     def yield_samples_by_characteristic(self, characteristic=None):
-        """Gets an iterator of matching samples for a given characteristic.
+        """ Gets an iterator of matching samples for a given characteristic.
 
         Args:
             characteristic: Sample characteristic
@@ -395,7 +394,7 @@ def yield_samples_by_characteristic(self, characteristic=None):
             return filter(lambda x: characteristic in x.characteristics, self.samples)
 
     def get_sample_by_characteristic(self, characteristic):
-        """Gets the first matching sample material for a given characteristic.
+        """ Gets the first matching sample material for a given characteristic.
 
         Args:
             characteristic: Sample characteristic
@@ -412,7 +411,7 @@ def get_sample_by_characteristic(self, characteristic):
             return None
 
     def yield_samples_by_factor_value(self, factor_value=None):
-        """Gets an iterator of matching samples for a given factor_value.
+        """ Gets an iterator of matching samples for a given factor_value.
 
         Args:
             factor_value: Sample factor value
@@ -427,7 +426,7 @@ def yield_samples_by_factor_value(self, factor_value=None):
             return filter(lambda x: factor_value in x.factor_values, self.samples)
 
     def get_sample_by_factor_value(self, factor_value):
-        """Gets the first matching sample material for a given factor_value.
+        """ Gets the first matching sample material for a given factor_value.
 
         Args:
             factor_value: Sample factor value
@@ -444,7 +443,7 @@ def get_sample_by_factor_value(self, factor_value):
             return None
 
     def get_sample_names(self):
-        """Gets all of the sample names.
+        """ Gets all the sample names.
 
         Returns:
             :obj:`list` of str.
@@ -466,7 +465,7 @@ def other_material(self, val):
             raise AttributeError("{}.other_material must be iterable containing Materials".format(type(self).__name__))
 
     def yield_materials_by_characteristic(self, characteristic=None):
-        """Gets an iterator of matching materials for a given characteristic.
+        """ Gets an iterator of matching materials for a given characteristic.
 
         Args:
             characteristic: Material characteristic
@@ -481,7 +480,7 @@ def yield_materials_by_characteristic(self, characteristic=None):
             return filter(lambda x: characteristic in x.characteristics, self.other_material)
 
     def get_material_by_characteristic(self, characteristic):
-        """Gets the first matching material material for a given
+        """ Gets the first matching material for a given
         characteristic.
 
         Args:

isatools/model/ontology_source.py

@@ -1,9 +1,10 @@
 from typing import Any, List
 
 from isatools.model.comments import Comment, Commentable
+from isatools.model.identifiable import Identifiable
 
 
-class OntologySource(Commentable):
+class OntologySource(Commentable, Identifiable):
     """An OntologySource describes the resource from which the value of an
     OntologyAnnotation is derived from.
 
@@ -18,10 +19,10 @@ class OntologySource(Commentable):
     """
 
     def __init__(
-        self, name: str, file: str = "", version: str = "", description: str = "", comments: List[Comment] = None
+        self, id_="", name: str = "", file: str = "", version: str = "", description: str = "", comments: List[Comment] = None
     ):
         super().__init__(comments)
-
+        self.id = id_
         self.__name = name
         self.__file = file
         self.__version = version
@@ -119,6 +120,7 @@ def __ne__(self, other):
 
     def to_dict(self, ld=False):
         ontology_source_ref = {
+            "@id": self.id,
             "name": self.name,
             "file": self.file,
             "version": self.version,
@@ -128,6 +130,7 @@ def to_dict(self, ld=False):
         return self.update_isa_object(ontology_source_ref, ld=ld)
 
     def from_dict(self, ontology_source):
+        self.id = ontology_source.get("@id","")
         self.name = ontology_source["name"] if "name" in ontology_source else ""
         self.file = ontology_source["file"] if "file" in ontology_source else ""
         self.version = ontology_source["version"] if "version" in ontology_source else ""

isatools/model/study.py

@@ -4,6 +4,7 @@
 from isatools.model.assay import Assay
 from isatools.model.comments import Commentable
 from isatools.model.factor_value import StudyFactor
+from isatools.model.identifiable import Identifiable
 from isatools.model.loader_indexes import loader_states as indexes
 from isatools.model.logger import log
 from isatools.model.mixins import MetadataMixin, StudyAssayMixin
@@ -17,7 +18,7 @@
 from isatools.model.source import Source
 
 
-class Study(Commentable, StudyAssayMixin, MetadataMixin, object):
+class Study(Commentable, Identifiable, StudyAssayMixin, MetadataMixin, object):
     """Study is the central unit, containing information on the subject under
     study, its characteristics and any treatments applied.
 
@@ -396,6 +397,7 @@ def to_dict(self, ld=False):
 
     def from_dict(self, study):
         indexes.reset_process()
+        self.id = study.get("@id", "")
         self.filename = study.get("filename", "")
         self.identifier = study.get("identifier", "")
         self.title = study.get("title", "")