From 604e6d7f9c1472c217195793d970b727b87591bf Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Fri, 30 Dec 2011 13:12:17 +0100
Subject: [PATCH] fix bug in table class
- fix assign column type as string (not str) if pattern doesn't match
- allow more complicated headers (with special characters)
- add some test cases
---
modules/base/pymod/table.py | 5 +++--
modules/base/tests/test_table.py | 13 +++++++++++++
.../tests/testfiles/ost-table-difficult-headers.tab | 8 ++++++++
modules/base/tests/testfiles/ost-table-notype.tab | 4 ++++
.../base/tests/testfiles/ost-table-unknown-type.tab | 4 ++++
5 files changed, 32 insertions(+), 2 deletions(-)
create mode 100644 modules/base/tests/testfiles/ost-table-difficult-headers.tab
create mode 100644 modules/base/tests/testfiles/ost-table-notype.tab
create mode 100644 modules/base/tests/testfiles/ost-table-unknown-type.tab
diff --git a/modules/base/pymod/table.py b/modules/base/pymod/table.py
index 8c5b13c59..3cc032943 100644
--- a/modules/base/pymod/table.py
+++ b/modules/base/pymod/table.py
@@ -487,7 +487,7 @@ class Table(object):
@staticmethod
def _LoadOST(stream_or_filename):
- fieldname_pattern=re.compile(r'(?P<name>[A-Za-z0-9_]+)(\[(?P<type>\w+)\])?')
+ fieldname_pattern=re.compile(r'(?P<name>[^[]+)(\[(?P<type>\w+)\])?')
if not hasattr(stream_or_filename, 'read'):
stream=open(stream_or_filename, 'r')
else:
@@ -510,7 +510,7 @@ class Table(object):
if match.group('type'):
fieldtypes.append(match.group('type'))
else:
- fieldtypes.append('str')
+ fieldtypes.append('string')
fieldnames.append(match.group('name'))
tab=Table(fieldnames, fieldtypes)
header=True
@@ -526,6 +526,7 @@ class Table(object):
for row in self.rows:
for idx in range(len(row)):
row[idx]=self._Coerce(row[idx], self.col_types[idx])
+
@staticmethod
def _LoadCSV(stream_or_filename, sep):
if not hasattr(stream_or_filename, 'read'):
diff --git a/modules/base/tests/test_table.py b/modules/base/tests/test_table.py
index 42276a657..1f1260bf6 100644
--- a/modules/base/tests/test_table.py
+++ b/modules/base/tests/test_table.py
@@ -713,6 +713,17 @@ class TestTable(unittest.TestCase):
tab.Sort('third', '+')
self.CompareDataFromDict(tab, {'first': [None,'foo','x'], 'second': [9,None,3], 'third': [3.3,2.2,None]})
+ def testLoadTableOSTUnknownType(self):
+ self.assertRaises(ValueError, Table.Load, os.path.join('testfiles','ost-table-unknown-type.tab'))
+
+ def testLoadTableOSTNoType(self):
+ tab = Table.Load(os.path.join('testfiles','ost-table-notype.tab'))
+ self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+
+ def testLoadOSTDifficultHeaders(self):
+ tab = Table.Load(os.path.join('testfiles','ost-table-difficult-headers.tab'))
+ self.assertEquals(tab.col_types, ['float','float','float','float','float'])
+
def testSaveLoadTableOST(self):
tab = self.CreateTestTable()
self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
@@ -738,6 +749,7 @@ class TestTable(unittest.TestCase):
self.assertRaises(IOError, Table.Load, os.path.join('testfiles','emptytable.tab'))
in_stream = open(os.path.join('testfiles','emptytable.csv'), 'r')
self.assertRaises(IOError, Table.Load, in_stream)
+
def testSaveLoadTableCSV(self):
tab = self.CreateTestTable()
self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
@@ -757,6 +769,7 @@ class TestTable(unittest.TestCase):
# check content
self.CompareDataFromDict(tab_loaded_stream, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
self.CompareDataFromDict(tab_loaded_fname, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
+
def testSaveLoadTablePickle(self):
tab = self.CreateTestTable()
self.CompareDataFromDict(tab, {'first': ['x','foo',None], 'second': [3,None,9], 'third': [None,2.2,3.3]})
diff --git a/modules/base/tests/testfiles/ost-table-difficult-headers.tab b/modules/base/tests/testfiles/ost-table-difficult-headers.tab
new file mode 100644
index 000000000..792a25971
--- /dev/null
+++ b/modules/base/tests/testfiles/ost-table-difficult-headers.tab
@@ -0,0 +1,8 @@
+cut-off[float] a_sangle[float] smoo:thing[float] 3O89.pdb.gz[float] 3P0K;pdbgz[float]
+1.0 20.0 0.0 0.5 0.5
+1.0 20.0 2.0 0.600685362782 0.774702862809
+1.0 20.0 4.0 0.749697277923 0.872928615954
+1.0 20.0 6.0 0.775949336433 0.864866900109
+1.0 20.0 8.0 0.673823016565 0.818450326527
+1.0 20.0 10.0 0.528419548581 0.779631093875
+1.0 20.0 12.0 0.463080015499 0.761846789747
diff --git a/modules/base/tests/testfiles/ost-table-notype.tab b/modules/base/tests/testfiles/ost-table-notype.tab
new file mode 100644
index 000000000..10f59019b
--- /dev/null
+++ b/modules/base/tests/testfiles/ost-table-notype.tab
@@ -0,0 +1,4 @@
+first second[int] third[float]
+x 3 NA
+foo NA 2.2
+NA 9 3.3
diff --git a/modules/base/tests/testfiles/ost-table-unknown-type.tab b/modules/base/tests/testfiles/ost-table-unknown-type.tab
new file mode 100644
index 000000000..69c79442b
--- /dev/null
+++ b/modules/base/tests/testfiles/ost-table-unknown-type.tab
@@ -0,0 +1,4 @@
+first[unknown] second[int] third[float]
+x 3 NA
+foo NA 2.2
+NA 9 3.3
--
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