Author: bugman
Date: Tue Mar 10 09:50:11 2015
New Revision: 27795
URL: http://svn.gna.org/viewcvs/relax?rev=27795&view=rev
Log:
Merged revisions 27793-27794 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r27793 | bugman | 2015-03-10 09:47:19 +0100 (Tue, 10 Mar 2015) | 11 lines
Converted the lib.sequence.validate_sequence() to the checking function
design.
This is the checking function design documented at
http://wiki.nmr-relax.com/Relax_source_design#The_check_.2A.28.29_functions.
The
validate_sequence() function has been renamed to check_sequence_func() and
the checking object is
called check_sequence. It removes the string processing hack to convert
RelaxErrors to
RelaxWarnings in the lib.sequence.read_spin_data() function, avoiding
strange messages such at
"RelaxWarning: ror: The sequence data in the line..." as seen in the
Sequence.test_bug_23372_read_csv system test.
........
r27794 | bugman | 2015-03-10 09:48:39 +0100 (Tue, 10 Mar 2015) | 3 lines
Small typo fix for the Sequence.test_bug_23372_read_csv system test.
........
Modified:
branches/nmrglue/ (props changed)
branches/nmrglue/lib/sequence.py
branches/nmrglue/test_suite/system_tests/sequence.py
Propchange: branches/nmrglue/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Mar 10 09:50:11 2015
@@ -1 +1 @@
-/trunk:1-27790
+/trunk:1-27794
Modified: branches/nmrglue/lib/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/lib/sequence.py?rev=27795&r1=27794&r2=27795&view=diff
==============================================================================
--- branches/nmrglue/lib/sequence.py (original)
+++ branches/nmrglue/lib/sequence.py Tue Mar 10 09:50:11 2015
@@ -28,6 +28,7 @@
from warnings import warn
# relax module imports.
+from lib.checks import Check
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxInvalidSeqError
from lib.io import extract_data, open_write_file, strip, write_data
@@ -81,6 +82,90 @@
# No code.
return '*'
+
+
+def check_sequence_func(data, spin_id_col=None, mol_name_col=None,
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None,
data_col=None, error_col=None):
+ """Test if the sequence data is valid.
+
+ The only function this performs is to raise a RelaxError if the data is
invalid.
+
+
+ @param data: The sequence data.
+ @type data: list of lists.
+ @keyword spin_id_col: The column containing the spin ID strings.
+ @type spin_id_col: int or None
+ @param mol_name_col: The column containing the molecule name
information.
+ @type mol_name_col: int or None
+ @param res_name_col: The column containing the residue name
information.
+ @type res_name_col: int or None
+ @param res_num_col: The column containing the residue number
information.
+ @type res_num_col: int or None
+ @param spin_name_col: The column containing the spin name information.
+ @type spin_name_col: int or None
+ @param spin_num_col: The column containing the spin number
information.
+ @type spin_num_col: int or None
+ """
+
+ # Spin ID.
+ if spin_id_col:
+ if len(data) < spin_id_col:
+ return RelaxInvalidSeqError(data, "the Spin ID data is missing")
+
+ # Molecule name data.
+ if mol_name_col:
+ if len(data) < mol_name_col:
+ return RelaxInvalidSeqError(data, "the molecule name data is
missing")
+
+ # Residue number data.
+ if res_num_col:
+ # No data in column.
+ if len(data) < res_num_col:
+ return RelaxInvalidSeqError(data, "the residue number data is
missing")
+
+ # Bad data in column.
+ try:
+ res_num = eval(data[res_num_col-1])
+ if not (res_num == None or isinstance(res_num, int)):
+ return RelaxInvalidSeqError(data, "the residue number data
'%s' is invalid" % data[res_num_col-1])
+ except:
+ return RelaxInvalidSeqError(data, "the residue number data '%s'
is invalid" % data[res_num_col-1])
+
+ # Residue name data.
+ if res_name_col:
+ if len(data) < res_name_col:
+ return RelaxInvalidSeqError(data, "the residue name data is
missing")
+
+ # Spin number data.
+ if spin_num_col:
+ # No data in column.
+ if len(data) < spin_num_col:
+ return RelaxInvalidSeqError(data, "the spin number data is
missing")
+
+ # Bad data in column.
+ try:
+ res_num = eval(data[res_num_col-1])
+ if not (res_num == None or isinstance(res_num, int)):
+ return RelaxInvalidSeqError(data, "the spin number data '%s'
is invalid" % data[res_num_col-1])
+ except:
+ return RelaxInvalidSeqError(data, "the spin number data '%s' is
invalid" % data[res_num_col-1])
+
+ # Spin name data.
+ if spin_name_col:
+ if len(data) < spin_name_col:
+ return RelaxInvalidSeqError(data, "the spin name data is
missing")
+
+ # Data.
+ if data_col:
+ if len(data) < data_col:
+ return RelaxInvalidSeqError(data, "the data is missing")
+
+ # Errors
+ if error_col:
+ if len(data) < error_col:
+ return RelaxInvalidSeqError(data, "the error data is missing")
+
+# Create the checking object.
+check_sequence = Check(check_sequence_func)
def read_spin_data(file=None, dir=None, file_data=None, spin_id_col=None,
mol_name_col=None, res_num_col=None, res_name_col=None, spin_num_col=None,
spin_name_col=None, data_col=None, error_col=None, sep=None, spin_id=None):
@@ -159,17 +244,7 @@
# Convert.
# Validate the sequence.
- try:
- validate_sequence(line, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col)
- except RelaxInvalidSeqError:
- # Extract the message string, without the RelaxError bit.
- msg = sys.exc_info()[1]
- string = msg.__str__()[12:-1]
-
- # Give a warning.
- warn(RelaxWarning(string))
-
- # Skip the line.
+ if not check_sequence(line, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col,
escalate=1):
continue
# Get the spin data from the ID.
@@ -272,87 +347,6 @@
# Hmmm, no data!
if missing_data:
raise RelaxError("No corresponding data could be found within the
file.")
-
-
-def validate_sequence(data, spin_id_col=None, mol_name_col=None,
res_num_col=None, res_name_col=None, spin_num_col=None, spin_name_col=None,
data_col=None, error_col=None):
- """Test if the sequence data is valid.
-
- The only function this performs is to raise a RelaxError if the data is
invalid.
-
-
- @param data: The sequence data.
- @type data: list of lists.
- @keyword spin_id_col: The column containing the spin ID strings.
- @type spin_id_col: int or None
- @param mol_name_col: The column containing the molecule name
information.
- @type mol_name_col: int or None
- @param res_name_col: The column containing the residue name
information.
- @type res_name_col: int or None
- @param res_num_col: The column containing the residue number
information.
- @type res_num_col: int or None
- @param spin_name_col: The column containing the spin name information.
- @type spin_name_col: int or None
- @param spin_num_col: The column containing the spin number
information.
- @type spin_num_col: int or None
- """
-
- # Spin ID.
- if spin_id_col:
- if len(data) < spin_id_col:
- raise RelaxInvalidSeqError(data, "the Spin ID data is missing")
-
- # Molecule name data.
- if mol_name_col:
- if len(data) < mol_name_col:
- raise RelaxInvalidSeqError(data, "the molecule name data is
missing")
-
- # Residue number data.
- if res_num_col:
- # No data in column.
- if len(data) < res_num_col:
- raise RelaxInvalidSeqError(data, "the residue number data is
missing")
-
- # Bad data in column.
- try:
- res_num = eval(data[res_num_col-1])
- if not (res_num == None or isinstance(res_num, int)):
- raise ValueError
- except:
- raise RelaxInvalidSeqError(data, "the residue number data '%s'
is invalid" % data[res_num_col-1])
-
- # Residue name data.
- if res_name_col:
- if len(data) < res_name_col:
- raise RelaxInvalidSeqError(data, "the residue name data is
missing")
-
- # Spin number data.
- if spin_num_col:
- # No data in column.
- if len(data) < spin_num_col:
- raise RelaxInvalidSeqError(data, "the spin number data is
missing")
-
- # Bad data in column.
- try:
- res_num = eval(data[res_num_col-1])
- if not (res_num == None or isinstance(res_num, int)):
- raise ValueError
- except:
- raise RelaxInvalidSeqError(data, "the spin number data '%s' is
invalid" % data[res_num_col-1])
-
- # Spin name data.
- if spin_name_col:
- if len(data) < spin_name_col:
- raise RelaxInvalidSeqError(data, "the spin name data is missing")
-
- # Data.
- if data_col:
- if len(data) < data_col:
- raise RelaxInvalidSeqError(data, "the data is missing")
-
- # Errors
- if error_col:
- if len(data) < error_col:
- raise RelaxInvalidSeqError(data, "the error data is missing")
def write_spin_data(file, dir=None, sep=None, spin_ids=None, mol_names=None,
res_nums=None, res_names=None, spin_nums=None, spin_names=None, force=False,
data=None, data_name=None, error=None, error_name=None,
float_format="%20.15g"):
Modified: branches/nmrglue/test_suite/system_tests/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/sequence.py?rev=27795&r1=27794&r2=27795&view=diff
==============================================================================
--- branches/nmrglue/test_suite/system_tests/sequence.py (original)
+++ branches/nmrglue/test_suite/system_tests/sequence.py Tue Mar 10
09:50:11 2015
@@ -52,7 +52,7 @@
self.assertEqual(len(cdp.mol[0].res), 2)
for spin, spin_id in spin_loop(return_id=True):
self.assertEqual(spin_id, seq[i])
- i += 0
+ i += 1
def test_load_protein_asp_atoms_from_pdb(self):
r27795 - in /branches/nmrglue: ./ lib/sequence.py test_suite/system_tests/sequence.py