Changes finalized and tested

isatools/isatab/dump/write.py

@@ -240,7 +240,13 @@ def write_assay_table_files(inv_obj, output_dir, write_factor_values=False):
 
  if not isinstance(inv_obj, Investigation):
  raise NotImplementedError
- protocol_types_dict = load_protocol_types_info()
+ yaml_dict = load_protocol_types_info()
+ protocol_types_dict = {}
+ for protocol, attributes in yaml_dict.items():
+ protocol_types_dict[protocol] = attributes
+ for synonym in attributes[SYNONYMS]:
+ protocol_types_dict[synonym] = attributes
+
  for study_obj in inv_obj.studies:
  for assay_obj in study_obj.assays:
  a_graph = assay_obj.graph
@@ -300,7 +306,8 @@ def flatten(current_list):
  else:
  protocol_type = node.executes_protocol.protocol_type.lower()
 
- if protocol_type in protocol_types_dict:
+ if protocol_type in protocol_types_dict and\
+ protocol_types_dict[protocol_type][HEADER]:
  oname_label = protocol_types_dict[protocol_type][HEADER]
  else:
  oname_label = None
@@ -360,7 +367,8 @@ def pbar(x):
  else:
  protocol_type = node.executes_protocol.protocol_type.lower()
 
- if protocol_type in protocol_types_dict:
+ if protocol_type in protocol_types_dict and\
+ protocol_types_dict[protocol_type][HEADER]:
  oname_label = protocol_types_dict[protocol_type][HEADER]
  else:
  oname_label = None

isatools/model/process.py

@@ -307,18 +307,18 @@ def from_assay_dict(self, process, technology_type):
  self.name = process.get('name', '')
  self.executes_protocol = indexes.get_protocol(process['executesProtocol']['@id'])
  self.load_comments(process.get('comments', []))
- allowed_protocol_type_terms = [
- "nucleic acid sequencing",
- "nmr spectroscopy",
- "mass spectrometry",
- "nucleic acid hybridization",
- "data transformation",
- "data normalization"
- ]
- if self.executes_protocol.protocol_type.term in allowed_protocol_type_terms or (
- self.executes_protocol.protocol_type.term == 'data collection'
- and technology_type.term == 'DNA microarray'):
- self.name = process['name']
+ # allowed_protocol_type_terms = [
+ #  "nucleic acid sequencing",
+ #  "nmr spectroscopy",
+ #  "mass spectrometry",
+ #  "nucleic acid hybridization",
+ #  "data transformation",
+ #  "data normalization"
+ # ]
+ # if self.executes_protocol.protocol_type.term in allowed_protocol_type_terms or (
+ #  self.executes_protocol.protocol_type.term == 'data collection'
+ #  and technology_type.term == 'DNA microarray'):
+ #  self.name = process['name']
 
  # Inputs / Outputs
  for io_data_target in ['inputs', 'outputs']:

isatools/model/protocol.py

@@ -283,14 +283,7 @@ def load_protocol_types_info() -> dict:
  """
  filepath = os.path.join(os.path.dirname(__file__), '..', 'resources', 'config', 'yaml', 'protocol-types.yml')
  with open(filepath) as yaml_file:
- yaml_dict = load(yaml_file, Loader=FullLoader)
-
- protocol_types_dict = {}
- for protocol, attributes in yaml_dict.items():
- protocol_types_dict[protocol] = attributes
- for synonym in attributes[SYNONYMS]:
- protocol_types_dict[synonym] = attributes
-
- return protocol_types_dict
+ return load(yaml_file, Loader=FullLoader)
+
 
 

isatools/resources/config/yaml/protocol-types.yml

@@ -1,20 +1,20 @@
 sample collection:
- header: Sample Name
+ header: 
  iri: http://purl.obolibrary.org/obo/OBI_0000659
  synonyms:
  - sample collection
  - sampling
  - aliquoting
 extraction:
- header: Extract Name
+ header: 
  iri: http://purl.obolibrary.org/obo/OBI_0302884
  synonyms:
  - extraction
  - metabolite extraction
  - intracellular metabolite extraction
  - extracelluar metabolite extraction
 labeling:
- header: Labeled Extract Name
+ header: 
  iri: http://purl.obolibrary.org/obo/OBI_0600038
  synonyms:
  - labeling

tests/model/test_protocol.py

@@ -246,4 +246,4 @@ class TestFunctions(TestCase):
  def test_load_protocol_types_info(self):
  yaml_config = load_protocol_types_info()
  self.assertTrue(isinstance(yaml_config, dict))
- self.assertTrue(len(yaml_config.keys()) == 15)
+ self.assertEqual(len(yaml_config.keys()), 16)