added source_type to Study Arm; tests needed #329

isatools/create/models.py

@@ -94,14 +94,18 @@
 with open(os.path.join(os.path.dirname(__file__), '..', 'resources', 'config', 'yaml',
                        'study-creator-config.yaml')) as yaml_file:
     yaml_config = yaml.load(yaml_file)
-default_ontology_source_reference = OntologySource(**yaml_config['study']['ontology_source_references'][0])
+default_ontology_source_reference = OntologySource(**yaml_config['study']['ontology_source_references'][1])
 
 DEFAULT_SOURCE_TYPE = Characteristic(
-    category=OntologyAnnotation(term='Material Type'),
+    category=OntologyAnnotation(
+        term='Study Subject',
+        term_source=default_ontology_source_reference,
+        term_accession='http://purl.obolibrary.org/obo/NCIT_C41189'
+    ),
     value=OntologyAnnotation(
-        term='subject',
+        term='Human',
         term_source=default_ontology_source_reference,
-        term_accession='0100051')
+        term_accession='http://purl.obolibrary.org/obo/NCIT_C14225')
 )
 
 ZFILL_WIDTH = 3
@@ -1597,34 +1601,49 @@ class StudyArm(object):
 
     ARM_MAP_ASSIGNMENT_ERROR = 'arm_map must be an OrderedDict'
 
-    def __init__(self, name, arm_map=None, group_size=0):
+    DEFAULT_SOURCE_TYPE = DEFAULT_SOURCE_TYPE
+
+    def __init__(self, name, arm_map=None, source_type=None, group_size=0):
+        """
+        The default constructor.
+        :param name: string
+        :param arm_map: OrderedDict - a StudyCell -> SampleAndAssayPlan ordered mapping
+        :param source_type: Characteristic/str - determines the "type" of the subjects/sources
+        :param group_size: int - a positive integer who specifies the number of subject in the Arm
+        """
         self.__name = ''
+        self.__source_type = None
         self.__group_size = None
         self.__arm_map = OrderedDict()
         self.name = name
         self.group_size = group_size
         if arm_map is not None:
             self.arm_map = arm_map
+        if source_type:
+            self.source_tye = source_type
 
     def __repr__(self):
         return '{0}.{1}(' \
                'name={name}, ' \
+               'source_type={source_type}, ' \
                'group_size={group_size}, ' \
                'cells={cells}, ' \
                'sample_assay_plans={sample_assay_plans})'.format(
-                    self.__class__.__module__, self.__class__.__name__, name=self.name, group_size=self.group_size,
+                    self.__class__.__module__, self.__class__.__name__, name=self.name,
+                    source_type=self.source_type, group_size=self.group_size,
                     cells=self.cells, sample_assay_plans=self.sample_assay_plans
                 )
 
     def __str__(self):
         return """"{1}(
                name={name},
+               source_type={source_type},
                group_size={group_size}, 
                cells={cells},
                sample_assay_plans={sample_assay_plans}
                )""".format(
                     self.__class__.__module__, self.__class__.__name__, name=self.name, group_size=self.group_size,
-                    cells=self.cells, sample_assay_plans=self.sample_assay_plans
+                    source_type=self.source_type, cells=self.cells, sample_assay_plans=self.sample_assay_plans
         )
 
     def __hash__(self):
@@ -1647,6 +1666,19 @@ def name(self, name):
             raise AttributeError('StudyArm name must be a string')
         self.__name = name
 
+    @property
+    def source_type(self):
+        if self.__source_type:
+            return self.__source_type
+        else:
+            return self.DEFAULT_SOURCE_TYPE
+
+    @source_type.setter
+    def source_type(self, source_type):
+        if not isinstance(source_type, (str, Characteristic)):
+            raise AttributeError('The source_type property must be either a string or a valid characteristic')
+        self.__source_type = source_type
+
     @property
     def group_size(self):
         return self.__group_size
@@ -1824,7 +1856,6 @@ def __init__(self, name='Study Design', source_type=DEFAULT_SOURCE_TYPE, study_a
         if study_arms:
             self.study_arms = study_arms
 
-
     @property
     def name(self):
         return self.__name
@@ -2010,7 +2041,7 @@ def _generate_samples(self, sources_map, sampling_protocol, performer, split_ass
     def _generate_isa_elements_from_node(node, assay_graph, processes=[], other_materials=[], data_files=[],
                                          previous_items=[], ix=0):
         log.debug('# processes: {0}'.format(len(processes)))
-        item = isa_objects_factory(node, ix)
+        item = isa_objects_factory(node, sequence_no=ix)
         if isinstance(item, Process):
             item.inputs = previous_items
             processes.append(item)

isatools/resources/config/yaml/study-creator-config.yaml

@@ -5,6 +5,10 @@ study:
       file: 'https://raw.githubusercontent.com/obi-ontology/obi/v2018-02-12/obi.owl'
       version: 'v2018-02-12'
       description: 'Ontology for Biomedical Investigations'
+    - name: 'NCIT',
+      file: 'http://purl.obolibrary.org/obo/ncit/releases/2019-03-02/ncit.owl'
+      version: '19.02d'
+      description: 'NCI Thesaurus OBO Edition'
   protocols:
     - name: 'sample collection'
       protocol_type: 'sample_collection'

tests/test_create_models_study_design.py

@@ -913,19 +913,20 @@ def test_repr(self):
 
     def test_str(self):
         qc = QualityControl()
-        self.assertEqual(str(qc), """QualityControl(
+        self.assertEqual(str(qc).replace(" ", ""), """QualityControl(
         pre_run_sample_type=None
         post_run_sample_type=None
         interspersed_sample_types=[]
-        )""")
+        )""".replace(" ", ""))
         qc = QualityControl(interspersed_sample_type=self.interspersed_sample_types,
                             pre_run_sample_type=self.pre_run_sample_type,
                             post_run_sample_type=self.post_run_sample_type)
-        self.assertEqual(str(qc), """QualityControl(
+        self.assertEqual(str(qc).replace(" ", ""), """QualityControl(
         pre_run_sample_type={0}
         post_run_sample_type={1}
-        interspersed_sample_types=[({2},{3})]
-        )""".format(self.pre_run_sample_type.id, self.post_run_sample_type.id, self.dummy_sample_type.id, 20))
+        interspersed_sample_types=[('{2}',{3})]
+        )""".format(self.pre_run_sample_type.id, self.post_run_sample_type.id, self.dummy_sample_type.id, 20)
+                         .replace(" ", ""))
 
 
 class AssayGraphTest(unittest.TestCase):