Merge pull request #556 from ptth222/protocol-types-refactor

Protocol types refactor

isatools/constants.py

@@ -1,4 +1,5 @@
 SYNONYMS = 'synonyms'
+HEADER = 'header'
 
 MATERIAL_LABELS = [
  'Source Name',

isatools/isatab/dump/write.py

@@ -3,7 +3,7 @@
 from pandas import DataFrame
 from numpy import nan
 
-from isatools.constants import SYNONYMS
+from isatools.constants import SYNONYMS, HEADER
 from isatools.model import (
  OntologyAnnotation,
  Investigation,
@@ -21,8 +21,7 @@
  get_pv_columns,
  get_fv_columns,
  get_characteristic_columns,
- get_object_column_map,
- get_column_header
+ get_object_column_map
 )
 
 
@@ -241,7 +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
@@ -296,17 +301,24 @@ def flatten(current_list):
  columns += flatten(map(lambda x: get_pv_columns(olabel, x),
  node.parameter_values))
  if node.executes_protocol.protocol_type:
- oname_label = get_column_header(
- node.executes_protocol.protocol_type.term,
- protocol_types_dict
- )
+ if isinstance(node.executes_protocol.protocol_type, OntologyAnnotation):
+ protocol_type = node.executes_protocol.protocol_type.term.lower()
+ else:
+ protocol_type = node.executes_protocol.protocol_type.lower()
+
+ 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
+
  if oname_label is not None:
  columns.append(oname_label)
- elif node.executes_protocol.protocol_type.term.lower() \
-  in protocol_types_dict["nucleic acid hybridization"][SYNONYMS]:
- columns.extend(
- ["Hybridization Assay Name",
-  "Array Design REF"])
+
+ if node.executes_protocol.protocol_type.term.lower() in \
+  protocol_types_dict["nucleic acid hybridization"][SYNONYMS]:
+ columns.append("Array Design REF")
+
  columns += flatten(
  map(lambda x: get_comment_column(olabel, x),
  node.comments))
@@ -350,19 +362,24 @@ def pbar(x):
  protocol_in_path_count += 1
  df_dict[olabel][-1] = node.executes_protocol.name
  if node.executes_protocol.protocol_type:
- oname_label = get_column_header(
- node.executes_protocol.protocol_type.term,
- protocol_types_dict
- )
+ if isinstance(node.executes_protocol.protocol_type, OntologyAnnotation):
+ protocol_type = node.executes_protocol.protocol_type.term.lower()
+ else:
+ protocol_type = node.executes_protocol.protocol_type.lower()
+
+ 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
+
  if oname_label is not None:
  df_dict[oname_label][-1] = node.name
 
- elif node.executes_protocol.protocol_type.term.lower() in \
- protocol_types_dict["nucleic acid hybridization"][SYNONYMS]:
- df_dict["Hybridization Assay Name"][-1] = \
- node.name
- df_dict["Array Design REF"][-1] = \
- node.array_design_ref
+ if node.executes_protocol.protocol_type.term.lower() in \
+ protocol_types_dict["nucleic acid hybridization"][SYNONYMS]:
+ df_dict["Array Design REF"][-1] = node.array_design_ref
+
  if node.date is not None:
  df_dict[olabel + ".Date"][-1] = node.date
  if node.performer is not None:

isatools/isatab/utils.py

@@ -515,32 +515,6 @@ def get_object_column_map(isatab_header, df_columns):
  return object_column_map
 
 
-def get_column_header(protocol_type_term, protocol_types_dict):
- column_header = None
- if protocol_type_term.lower() in \
- protocol_types_dict["nucleic acid sequencing"][SYNONYMS] \
- + protocol_types_dict["phenotyping"][SYNONYMS] \
- + protocol_types_dict["data acquisition"][SYNONYMS]:
- column_header = "Assay Name"
- elif protocol_type_term.lower() in protocol_types_dict["data collection"][SYNONYMS]:
- column_header = "Scan Name"
- elif protocol_type_term.lower() in protocol_types_dict["mass spectrometry"][SYNONYMS]:
- column_header = "MS Assay Name"
- elif protocol_type_term.lower() in protocol_types_dict["nmr spectroscopy"][SYNONYMS]:
- column_header = "NMR Assay Name"
- elif protocol_type_term.lower() in \
- protocol_types_dict["data transformation"][SYNONYMS] \
- + protocol_types_dict["sequence analysis data transformation"][SYNONYMS] \
- + protocol_types_dict["metabolite identification"][SYNONYMS] \
- + protocol_types_dict["protein identification"][SYNONYMS]:
- column_header = "Data Transformation Name"
- elif protocol_type_term.lower() in protocol_types_dict["normalization"][SYNONYMS]:
- column_header = "Normalization Name"
- if protocol_type_term.lower() == "unknown protocol":
- column_header = "Unknown Protocol Name"
- return column_header
-
-
 def get_value_columns(label, x):
  """ Generates the appropriate columns based on the value of the object.
  For example, if the object's .value value is an OntologyAnnotation,

isatools/model/process.py

@@ -307,18 +307,6 @@ 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']
 
  # Inputs / Outputs
  for io_data_target in ['inputs', 'outputs']:

isatools/model/protocol.py

@@ -2,6 +2,7 @@
 from collections.abc import Iterable
 from pprint import pprint
 from yaml import load, FullLoader
+from isatools.constants import SYNONYMS
 from isatools.model.comments import Commentable
 from isatools.model.ontology_annotation import OntologyAnnotation
 from isatools.model.protocol_parameter import ProtocolParameter
@@ -283,3 +284,6 @@ 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:
  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
@@ -83,4 +83,8 @@ metabolite identification:
 protein identification:
  header: Data Transformation Name
  synonyms:
- - protein identification
+ - protein identification
+unknown protocol:
+ header: Unknown Protocol Name
+ synonyms:
+ - unknown protocol

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)