Merge pull request #453 from ISA-tools/DomModelRefactor

Dom model refactor

.github/workflows/buildandtestpython.yml

@@ -32,7 +32,7 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-      - name: Test with python unittests
+      - name: Test with python unittest
         run: |
           behave --no-capture --no-capture-stderr --format=progress features/isa-file-handler.feature
           coverage run -m unittest discover -s tests/

isatools/create/model.py

@@ -2222,8 +2222,8 @@ def _generate_samples_and_assays(self, sources_map, sampling_protocol, performer
                                 derives_from=[source],
                                 comments=[is_treatment_comment]
                             )
-                            if sample_type not in characteristic_categories:
-                                characteristic_categories.append(sample_type)
+                            if sample_type.category not in characteristic_categories:
+                                characteristic_categories.append(sample_type.category)
 
                             sample_batches[sample_node].append(sample)
                             sample_count += 1
@@ -2320,8 +2320,8 @@ def _generate_isa_elements_from_node(
             other_materials.append(item)
             # characteristic_categories.append(item.characteristics)
             for charx in item.characteristics:
-                if charx not in characteristic_categories:
-                    characteristic_categories.append(charx)
+                if charx.category not in characteristic_categories:
+                    characteristic_categories.append(charx.category)
 
         elif isinstance(item, DataFile):
             data_files.append(item)
@@ -2570,7 +2570,7 @@ def generate_isa_study(self, identifier=None):
 
         # setting the `characteristic_categories` associated to study and required for isajson loading
         # study_charac_categories = []
-        study.characteristic_categories.append(DEFAULT_SOURCE_TYPE)
+        study.characteristic_categories.append(DEFAULT_SOURCE_TYPE.category)
         study.factors, new_protocols, study.samples, study_charac_categories, study.assays, study.process_sequence, \
             study.ontology_source_references = \
             self._generate_samples_and_assays(

isatools/isajson/__init__.py

@@ -0,0 +1,9 @@
+"""Functions for reading, writing and validating ISA-JSON.
+
+Don't forget to read the ISA-JSON spec:
+https://isa-specs.readthedocs.io/en/latest/isajson.html
+"""
+
+from isatools.isajson.load import load
+from isatools.isajson.dump import ISAJSONEncoder
+from isatools.isajson.validate import validate, batch_validate, default_config_dir, load_config

isatools/isajson/dump.py

@@ -0,0 +1,10 @@
+from json import JSONEncoder
+
+
+class ISAJSONEncoder(JSONEncoder):
+    def default(self, o):
+        if hasattr(o, 'to_dict'):
+            method = getattr(o, 'to_dict')
+            if callable(method):
+                return o.to_dict()
+        return JSONEncoder.default(self, o)

isatools/isajson/load.py

@@ -0,0 +1,15 @@
+import json
+
+from isatools.model import Investigation
+
+
+def load(fp):
+    """Loads an ISA-JSON file and returns an Investigation object.
+
+    :param fp: A file-like object or a string containing the JSON data.
+    :return: An Investigation object.
+    """
+    investigation_json = json.load(fp)
+    investigation = Investigation()
+    investigation.from_dict(investigation_json)
+    return investigation