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extracted get_header_name() method to fix bug on protocol type mapping
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‎isatools/isatab.py

+39-51
Original file line numberDiff line numberDiff line change
@@ -1406,33 +1406,11 @@ def flatten(l): return [item for sublist in l for item in sublist]
14061406
protrefcount += 1
14071407
columns += flatten(map(lambda x: get_pv_columns(olabel, x),
14081408
node.parameter_values))
1409-
oname_label = None
14101409
if node.executes_protocol.protocol_type:
1411-
if node.executes_protocol.protocol_type.term.lower() in \
1412-
protocol_types_dict["nucleic acid sequencing"][SYNONYMS] \
1413-
+ protocol_types_dict["phenotyping"][SYNONYMS]:
1414-
oname_label = "Assay Name"
1415-
elif node.executes_protocol.protocol_type.term.lower() in \
1416-
protocol_types_dict["data collection"][SYNONYMS]:
1417-
oname_label = "Scan Name"
1418-
elif node.executes_protocol.protocol_type.term.lower() in \
1419-
protocol_types_dict["mass spectrometry"][SYNONYMS]:
1420-
oname_label = "MS Assay Name"
1421-
elif node.executes_protocol.protocol_type.term.lower() in \
1422-
protocol_types_dict["nmr spectroscopy"][SYNONYMS]:
1423-
oname_label = "NMR Assay Name"
1424-
elif node.executes_protocol.protocol_type.term.lower() in \
1425-
protocol_types_dict["data transformation"][SYNONYMS]:
1426-
oname_label = "Data Transformation Name"
1427-
elif node.executes_protocol.protocol_type.term.lower() in \
1428-
protocol_types_dict["sequence analysis data transformation"][SYNONYMS]:
1429-
oname_label = "Normalization Name"
1430-
elif node.executes_protocol.protocol_type.term.lower() in \
1431-
protocol_types_dict["normalization"][SYNONYMS]:
1432-
oname_label = "Normalization Name"
1433-
if node.executes_protocol.protocol_type.term.lower() \
1434-
== "unknown protocol":
1435-
oname_label = "Unknown Protocol Name"
1410+
oname_label = get_column_header(
1411+
node.executes_protocol.protocol_type.term,
1412+
protocol_types_dict
1413+
)
14361414
if oname_label is not None:
14371415
columns.append(oname_label)
14381416
elif node.executes_protocol.protocol_type.term.lower() \
@@ -1492,32 +1470,11 @@ def pbar(x): return x
14921470
node.executes_protocol.name
14931471
)
14941472
df_dict[olabel][-1] = node.executes_protocol.name
1495-
oname_label = None
14961473
if node.executes_protocol.protocol_type:
1497-
if node.executes_protocol.protocol_type.term.lower() in \
1498-
protocol_types_dict["nucleic acid sequencing"][SYNONYMS]:
1499-
oname_label = "Assay Name"
1500-
elif node.executes_protocol.protocol_type.term.lower() in \
1501-
protocol_types_dict["data collection"][SYNONYMS]:
1502-
oname_label = "Scan Name"
1503-
elif node.executes_protocol.protocol_type.term.lower() in \
1504-
protocol_types_dict["mass spectrometry"][SYNONYMS]:
1505-
oname_label = "MS Assay Name"
1506-
elif node.executes_protocol.protocol_type.term.lower() in \
1507-
protocol_types_dict["nmr spectroscopy"][SYNONYMS]:
1508-
oname_label = "NMR Assay Name"
1509-
elif node.executes_protocol.protocol_type.term.lower() in \
1510-
protocol_types_dict["data transformation"][SYNONYMS]:
1511-
oname_label = "Data Transformation Name"
1512-
elif node.executes_protocol.protocol_type.term.lower() in \
1513-
protocol_types_dict["sequence analysis data transformation"][SYNONYMS]:
1514-
oname_label = "Data Transformation Name"
1515-
elif node.executes_protocol.protocol_type.term.lower() in \
1516-
protocol_types_dict["normalization"][SYNONYMS]:
1517-
oname_label = "Normalization Name"
1518-
if node.executes_protocol.protocol_type.term.lower() == \
1519-
"unknown protocol":
1520-
oname_label = "Unknown Protocol Name"
1474+
oname_label = get_column_header(
1475+
node.executes_protocol.protocol_type.term,
1476+
protocol_types_dict
1477+
)
15211478
if oname_label is not None:
15221479
df_dict[oname_label][-1] = node.name
15231480
elif node.executes_protocol.protocol_type.term.lower() in \
@@ -1643,6 +1600,37 @@ def pbar(x): return x
16431600
encoding='utf-8')
16441601

16451602

1603+
def get_column_header(protocol_type_term, protocol_types_dict):
1604+
column_header = None
1605+
if protocol_type_term.lower() in \
1606+
protocol_types_dict["nucleic acid sequencing"][SYNONYMS] \
1607+
+ protocol_types_dict["phenotyping"][SYNONYMS] \
1608+
+ protocol_types_dict["data acquisition"][SYNONYMS]:
1609+
column_header = "Assay Name"
1610+
elif protocol_type_term.lower() in \
1611+
protocol_types_dict["data collection"][SYNONYMS]:
1612+
column_header = "Scan Name"
1613+
elif protocol_type_term.lower() in \
1614+
protocol_types_dict["mass spectrometry"][SYNONYMS]:
1615+
column_header = "MS Assay Name"
1616+
elif protocol_type_term.lower() in \
1617+
protocol_types_dict["nmr spectroscopy"][SYNONYMS]:
1618+
column_header = "NMR Assay Name"
1619+
elif protocol_type_term.lower() in \
1620+
protocol_types_dict["data transformation"][SYNONYMS] \
1621+
+ protocol_types_dict["sequence analysis data transformation"][SYNONYMS] \
1622+
+ protocol_types_dict["metabolite identification"][SYNONYMS] \
1623+
+ protocol_types_dict["protein identification"][SYNONYMS]:
1624+
column_header = "Data Transformation Name"
1625+
elif protocol_type_term.lower() in \
1626+
protocol_types_dict["normalization"][SYNONYMS]:
1627+
column_header = "Normalization Name"
1628+
if protocol_type_term.lower() \
1629+
== "unknown protocol":
1630+
column_header = "Unknown Protocol Name"
1631+
return column_header
1632+
1633+
16461634
def get_value_columns(label, x):
16471635
"""Generates the appropriate columns based on the value of the object.
16481636
For example, if the object's .value value is an OntologyAnnotation,

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