extending assay deserialiser

isatools/isajson/load.py

@@ -473,6 +473,7 @@ def get_parameter_value(p_val_dict):
                 )
                 units_dict[unit.id] = unit
                 assay.units.append(unit)
+
             data_dict = dict()
             for data_json in assay_json["dataFiles"]:
                 data_file = DataFile(
@@ -487,9 +488,11 @@ def get_parameter_value(p_val_dict):
                 except KeyError:
                     data_file.derives_from = None
                 assay.data_files.append(data_file)
+
             for sample_json in assay_json["materials"]["samples"]:
                 sample = samples_dict[sample_json["@id"]]
                 assay.samples.append(sample)
+
             for assay_characteristics_category_json in assay_json["characteristicCategories"]:
                 characteristic_category = OntologyAnnotation(
                     # id_=assay_characteristics_category_json["characteristicType"]["@id"],
@@ -501,6 +504,7 @@ def get_parameter_value(p_val_dict):
                 )
                 study.characteristic_categories.append(characteristic_category)
                 categories_dict[characteristic_category.id] = characteristic_category
+
             other_materials_dict = dict()
             for other_material_json in assay_json["materials"]["otherMaterials"]:
                 material_name = other_material_json["name"].replace("labeledextract-", "").replace("extract-", "")
@@ -542,6 +546,7 @@ def get_parameter_value(p_val_dict):
                     material.characteristics.append(characteristic)
                 assay.other_material.append(material)
                 other_materials_dict[material.id] = material
+
             for assay_process_json in assay_json["processSequence"]:
                 process = Process(
                     id_=assay_process_json["@id"],

isatools/model/assay.py

@@ -187,7 +187,7 @@ def to_dict(self):
             "unitCategories": [unit.to_dict() for unit in self.units],
             "comments": [comment.to_dict() for comment in self.comments],
             "materials": {
-                "samples": [sample.to_dict() for sample in self.samples],
+                "samples": [{"@id": sample.id} for sample in self.samples],
                 "otherMaterials": [mat.to_dict() for mat in self.other_material]
             },
             "dataFiles": [file.to_dict() for file in self.data_files],
@@ -219,3 +219,22 @@ def from_dict(self, assay):
             unit.from_dict(unit_data)
             self.units.append(unit)
             indexes.add_unit(unit)
+
+        # data files
+        indexes.data_files = {}
+        for data_file_data in assay.get('dataFiles', []):
+            data_file = DataFile()
+            data_file.from_dict(data_file_data)
+            self.data_files.append(data_file)
+            indexes.add_data_file(data_file)
+
+        # samples
+        for sample_data in assay.get('materials', {}).get('samples', []):
+            self.samples.append(indexes.get_sample(sample_data['@id']))
+
+        # characteristic categories
+        for characteristic_category_data in assay.get('characteristicCategories', []):
+            characteristic_category = OntologyAnnotation()
+            characteristic_category.from_dict(characteristic_category_data['characteristicType'])
+            self.characteristic_categories.append(characteristic_category)
+            indexes.add_characteristic_category(characteristic_category)

isatools/model/datafile.py

@@ -105,6 +105,14 @@ def to_dict(self):
             "comments": [comment.to_dict() for comment in self.comments]
         }
 
+    def from_dict(self, data_file):
+        self.id = data_file.get('@id', '')
+        self.filename = data_file.get('name', '')
+        self.label = data_file.get('type', '')
+        self.load_comments(data_file.get('comments', []))
+
+        # TODO : missing generated_from property in dump/load methods
+
 
 class RawDataFile(DataFile):
     """Represents a raw data file in an experimental graph."""

isatools/model/loader_indexes.py

@@ -34,6 +34,7 @@ def init(self):
         self.sources = {}
         self.processes = {}
         self.term_sources = {}
+        self.data_files = {}
     return init
 
 
@@ -48,7 +49,8 @@ def to_str(self):
                 "samples: {indexes.samples},\n\t"
                 "sources: {indexes.sources},\n\t"
                 "processes: {indexes.processes},\n\t"
-                "term_sources: {indexes.term_sources}").format(indexes=self)
+                "term_sources: {indexes.term_sources},\n\t"
+                "data_files: {indexes.data_files}").format(indexes=self)
     return to_str
 
 
@@ -85,7 +87,6 @@ def add_term_source(self, item):
 
 def make_get_term_source():
     def get_term_source(self, name):
-        print(self.term_sources.keys())
         return self.term_sources[name]
     return get_term_source
 
@@ -98,7 +99,8 @@ def get_term_source(self, name):
     "unit": "units",
     "sample": "samples",
     "source": "sources",
-    'process': 'processes'
+    'process': 'processes',
+    'data_file': 'data_files'
 }
 
 methods = {
@@ -117,10 +119,10 @@ def get_term_source(self, name):
     methods['add_%s' % field_name] = make_add_resolver(field)
 
 # parameters of type are 1. class name 2. inheritance as tuple 3. methods and attributes
-Store = type('LoaderStore', (), methods)
-loader_states = Store()
+LoaderStore = type('LoaderStore', (), methods)
+loader_states = LoaderStore()
 
 
 def new_store():
-    return Store()
+    return LoaderStore()
 

isatools/model/sample.py

@@ -156,7 +156,7 @@ def to_dict(self):
 
     def from_dict(self, sample):
         self.id = sample.get('@id', '')
-        self.name = sample.get('name', '')
+        self.name = sample.get('name', '').replace('sample-', '-')
         self.load_comments(sample.get('comments', []))
 
         # characteristics

isatools/model/source.py

@@ -105,7 +105,7 @@ def to_dict(self):
 
     def from_dict(self, source):
         self.id = source.get('@id', '')
-        self.name = source.get('name', '')
+        self.name = source.get('name', '').replace("source-", "")
         self.load_comments(source.get('comments', []))
 
         # characteristics

tests/model/test_assay.py

@@ -3,6 +3,9 @@
 from isatools.model.assay import Assay
 from isatools.model.datafile import DataFile
 from isatools.model.ontology_annotation import OntologyAnnotation
+from isatools.model.ontology_source import OntologySource
+from isatools.model.sample import Sample
+from isatools.model.loader_indexes import loader_states as indexes
 
 
 class TestAssay(TestCase):
@@ -153,28 +156,40 @@ def test_to_dict(self):
         assay.from_dict(expected_dict)
         self.assertEqual(assay.to_dict(), expected_dict)
 
+        expected_dict['materials']['samples'] = [{"@id": 'my_sample'}]
+        indexes.samples = {'my_sample': Sample(id_='my_sample')}
+        assay = Assay()
+        assay.from_dict(expected_dict)
+        self.assertEqual(assay.to_dict(), expected_dict)
 
+        # Data Files
+        expected_dict['dataFiles'] = [
+            {
+                "@id": 'my_data_file',
+                "name": "filename",
+                "type": "RawDataFile",
+                "comments": []
+            }
+        ]
+        assay = Assay()
+        assay.from_dict(expected_dict)
+        self.assertEqual(assay.to_dict(), expected_dict)
 
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+        # Characteristic Categories
+        expected_dict['characteristicCategories'] = [
+            {
+                '@id': '#characteristic_category/test_id',
+                'characteristicType': {
+                    '@id': 'test_id',
+                    'annotationValue': 'test_term',
+                    'termSource': 'term_source1',
+                    'termAccession': '',
+                    'comments': []
+                }
+            }
+        ]
+        indexes.term_sources = {'term_source1': OntologySource(name='term_source1')}
+        assay = Assay()
+        assay.from_dict(expected_dict)
+        self.assertEqual(assay.to_dict(), expected_dict)
 

tests/model/test_datafile.py

@@ -1,5 +1,5 @@
 from unittest import TestCase
-from re import sub, compile
+from re import sub
 
 from isatools.model.datafile import *
 from isatools.model.sample import Sample
@@ -67,6 +67,23 @@ def test_equalities(self):
         self.assertTrue(first_datafile == second_datafile)
         self.assertTrue(self.datafile != first_datafile)
 
+    def test_from_dict(self):
+        expected_dict = {
+            "@id": 'my_data_file',
+            "name": "filename",
+            "type": "RawDataFile",
+            "comments": []
+        }
+        data_file = DataFile()
+        data_file.from_dict(expected_dict)
+        self.assertEqual(data_file.to_dict(), expected_dict)
+
+        raw_data_file = RawDataFile()
+        raw_data_file.from_dict(expected_dict)
+        self.assertEqual(raw_data_file.to_dict(), expected_dict)
+        self.assertEqual(raw_data_file.to_dict(), data_file.to_dict())
+        self.assertNotEqual(raw_data_file, data_file)
+
 
 class TestSubDataFile(TestCase):
 

tests/model/test_load_indexes.py

@@ -57,5 +57,6 @@ def test_methods(self):
                            "samples: {},\n\t"
                            "sources: {},\n\t"
                            "processes: {},\n\t"
-                           "term_sources: {}")
+                           "term_sources: {},\n\t"
+                           "data_files: {}")
         self.assertEqual(expected_string, str(indexes))

tests/model/test_study.py

@@ -449,20 +449,28 @@ def test_dict(self):
                 {
                     "characteristicCategories": [
                         {
-                            "@id": "my_cat",
-                            "annotationValue": "value",
-                            "termAccession": "123",
-                            "comments": []
+                            '@id': '#characteristic_category/test_id',
+                            'characteristicType': {
+                                '@id': 'test_id',
+                                'annotationValue': 'test_term',
+                                'termSource': '',
+                                'termAccession': '',
+                                'comments': []
+                            }
                         }
                     ]
                 },
                 {
                     "characteristicCategories": [
                         {
-                            "@id": "my_cat2",
-                            "annotationValue": "value2",
-                            "termAccession": "456",
-                            "comments": []
+                            '@id': '#characteristic_category/test_id',
+                            'characteristicType': {
+                                '@id': 'my_cat2',
+                                'annotationValue': 'value2',
+                                'termSource': '',
+                                'termAccession': '456',
+                                'comments': []
+                            }
                         }
                     ]
                 }