Merge pull request #531 from ptth222/check-protocol-fields-update

Fairly significant changes to check_protocol_fields

isatools/isatab/validate/rules/rules_40xx.py

@@ -254,30 +254,22 @@ def pairwise(iterable):
  a, b = tee(iterable)
  next(b, None)
  return zip(a, b)
-
- proto_ref_index = [i for i in table.columns if 'protocol ref' in i.lower()]
- result = True
- for each in proto_ref_index:
- prots_found = set()
- for cell in table[each]:
- prots_found.add(cell)
- if len(prots_found) > 1:
- log.warning("(W) Multiple protocol references {} are found in {}".format(prots_found, each))
- log.warning("(W) Only one protocol reference should be used in a Protocol REF column.")
- result = False
- if result:
- field_headers = [i for i in table.columns
- if i.lower().endswith(' name')
- or i.lower().endswith(' data file')
- or i.lower().endswith(' data matrix file')]
- protos = [i for i in table.columns if i.lower() == 'protocol ref']
- if len(protos) > 0:
- last_proto_index = table.columns.get_loc(protos[len(protos) - 1])
- else:
- last_proto_index = -1
- last_mat_or_dat_index = table.columns.get_loc(field_headers[len(field_headers) - 1])
- if last_proto_index > last_mat_or_dat_index:
- log.warning("(W) Protocol REF column without output in file '" + table.filename + "'")
+
+ field_headers = [i for i in table.columns
+ if i.lower().endswith(' name')
+ or i.lower().endswith(' data file')
+ or i.lower().endswith(' data matrix file')]
+ protos = [i for i in table.columns if i.lower() == 'protocol ref']
+ if len(protos) > 0:
+ last_proto_index = table.columns.get_loc(protos[len(protos) - 1])
+ else:
+ last_proto_index = -1
+ last_mat_or_dat_index = table.columns.get_loc(field_headers[len(field_headers) - 1])
+ if last_proto_index > last_mat_or_dat_index:
+ spl = "(W) Protocol REF column is not followed by a material or data node in file '" + table.filename + "'"
+ validator.add_warning(message="Missing Protocol Value", supplemental=spl, code=1007)
+ log.warning(spl)
+ if cfg.get_isatab_configuration():
  for left, right in pairwise(field_headers):
  cleft = None
  cright = None
@@ -294,25 +286,22 @@ def pairwise(iterable):
  fprotos_headers = [i for i in raw_headers if 'protocol ref' in i.lower()]
  fprotos = list()
  for header in fprotos_headers:
- proto_name = table.iloc[0][header]
- try:
- proto_type = proto_map[proto_name]
- fprotos.append(proto_type)
- except KeyError:
- spl = ("Could not find protocol type for protocol name '{}', trying to validate_rules against name "
- "only").format(proto_name)
- validator.add_warning(message="Missing Protocol declaration", supplemental=spl, code=1007)
- log.warning("(W) {}".format(spl))
- fprotos.append(proto_name)
+ proto_names = list(table.loc[:, header].unique())
+ for proto_name in proto_names:
+ proto_type = proto_map.get(proto_name)
+ if not proto_type and proto_name:
+ spl = ("Could not find protocol type for protocol name '{}' in file '{}'" ).format(proto_name, table.filename)
+ validator.add_warning(message="Missing Protocol Declaration", supplemental=spl, code=1007)
+ log.warning("(W) {}".format(spl))
+ else:
+ fprotos.append(proto_type)
  invalid_protos = set(cprotos) - set(fprotos)
  if len(invalid_protos) > 0:
  spl = ("Protocol(s) of type {} defined in the ISA-configuration expected as a between '{}' and "
  "'{}' but has not been found, in the file '{}'")
  spl = spl.format(str(list(invalid_protos)), cleft.header, cright.header, table.filename)
  validator.add_warning(message="Missing Protocol declaration", supplemental=spl, code=1007)
  log.warning("(W) {}".format(spl))
- result = False
- return result
 
 
 def load_table_checks(df, filename):