def testSupportedPostfixes():
names = "mz mzmin mzmax mz0 mzmin0 mzmax0 mz1 mzmax1 mzmin__0 mzmax__0 mz__0 "\
"mzmax3 mz4 mzmin4".split()
t = Table._create(names, [float] * len(names), [])
assert len(t.supportedPostfixes(["mz"])) == len(names)
assert t.supportedPostfixes(["mz", "mzmin"]) == ["", "0", "4", "__0"]
assert t.supportedPostfixes(["mz", "mzmin", "mzmax"]) == ["", "0", "__0"]
def test_removePostfixes():
t = Table._create(["abb__0", "bcb__0"], [str] * 2, ["%s"] * 2)
assert t.getColNames() == ["abb__0", "bcb__0"]
t.removePostfixes()
assert t.getColNames() == ["abb", "bcb"]
t.removePostfixes("bb", "cb")
assert t.getColNames() == ["a", "b"]
try:
t.print_()
t.removePostfixes("a", "b")
t.print_()
except:
pass
else:
assert False, "expected exception"
def loadCSV(path=None, sep=";", keepNone = False, **specialFormats):
# local import in order to keep namespaces clean
import ms
import csv, os.path, sys, re
from libms.DataStructures.Table import (Table, common_type_for,\
bestConvert, guessFormatFor)
if isinstance(path, unicode):
path = path.encode(sys.getfilesystemencoding())
elif path is None:
path = ms.askForSingleFile(extensions=["csv"])
if path is None:
return None
with open(path,"r") as fp:
# remove clutter at right margin
reader = csv.reader(fp, delimiter=sep)
# reduce multiple spaces to single underscore
colNames = [ re.sub(" +", "_", n.strip()) for n in reader.next()]
if keepNone:
conv = bestConvert
else:
conv = lambda v: None if v=="None" else bestConvert(v)
rows = [ [conv(c.strip()) for c in row] for row in reader]
columns = [[row[i] for row in rows] for i in range(len(colNames))]
types = [common_type_for(col) for col in columns]
#defaultFormats = {float: "%.2f", str: "%s", int: "%d"}
formats = dict([(name, guessFormatFor(name,type_)) for (name, type_)\
in zip(colNames, types)])
formats.update(specialFormats)
formats = [formats[n] for n in colNames]
title = os.path.basename(path)
meta = dict(loaded_from=os.path.abspath(path))
return Table._create(colNames, types, formats, rows, title, meta)
def _build_starttable(tables, force_merge):
colname_orders = []
for table in tables:
colname_orders.append(table._colNames)
colum_names = _topo_sort_with_in_order(colname_orders)
if colum_names is None:
raise Exception("could not combine all column names to a "\
"consistent order. you have to provide a reference table")
types = dict()
for table in tables:
for name in table._colNames:
type_ = table.getType(name)
if types.get(name, type_) != type_:
if not force_merge:
raise Exception("type conflictfor column %s" % name)
print "type conflict:",name, types.get(name, type_), type_
types[name] = type_
formats = dict()
for table in tables:
for name in table._colNames:
format_ = table.getFormat(name)
if formats.get(name, format_) != format_:
if not force_merge:
raise Exception("format conflict for column %s" % name)
print "format conflict:", name, formats.get(name, format_), format_
formats[name] = format_
final_types = [types.get(n) for n in colum_names]
final_formats = [formats.get(n) for n in colum_names]
prototype = Table._create(colum_names, final_types, final_formats)
return prototype, colum_names
