obi cat: fixed a bug introduced in 3.0.0b28 and switch to version

3.0.0b33

python/obitools3/commands/cat.pyx

@@ -4,7 +4,7 @@ from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
 from obitools3.dms import DMS
 from obitools3.dms.view.view cimport View
 from obitools3.uri.decode import open_uri
-from obitools3.apps.optiongroups import addMinimalOutputOption
+from obitools3.apps.optiongroups import addMinimalOutputOption, addNoProgressBarOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
 from obitools3.utils cimport str2bytes
@@ -28,6 +28,7 @@ __title__="Concatenate views."
 def addOptions(parser):
     
     addMinimalOutputOption(parser)
+    addNoProgressBarOption(parser)
 
     group=parser.add_argument_group('obi cat specific options')
 

python/obitools3/commands/export.pyx

@@ -89,7 +89,7 @@ def run(config):
 
     if pb is not None:
         pb(i, force=True)
-    print("", file=sys.stderr)
+        print("", file=sys.stderr)
 
     # TODO save command in input dms?
     

python/obitools3/commands/test.pyx

@@ -23,6 +23,7 @@ from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
 import shutil
 import string
 import random
+import sys
 from cpython.exc cimport PyErr_CheckSignals
 
 
@@ -366,7 +367,7 @@ def random_new_view(config, infos, first=False):
             infos['view'] = View_NUC_SEQS.new(infos['dms'], random_unique_name(infos), comments=random_comments(config))   # TODO quality column
         else :
             infos['view'] = View.new(infos['dms'], random_unique_name(infos), comments=random_comments(config))   # TODO quality column
-        
+        infos['view'].write_config(config, "test", infos["command_line"], input_dms_name=[infos['dms'].name], input_view_name=["random"])
     print_test(config, repr(infos['view']))
     if v_to_clone is not None :
         if line_selection is None:
@@ -497,7 +498,8 @@ def run(config):
                                     (b"OBI_SEQ", False): random_seq, (b"OBI_SEQ", True): random_seq_tuples,
                                     (b"OBI_STR", False): random_bytes, (b"OBI_STR", True): random_bytes_tuples
                                   },
-             'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view]
+             'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view],
+             'command_line': " ".join(sys.argv[1:])
             }
  
     # TODO ???

python/obitools3/commands/uniq.pyx

@@ -354,6 +354,9 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
         key = mergedKeys[k]
         merged_col_name = mergedKeys_m[k]
         
+        if merged_infos[merged_col_name]['nb_elts'] == 1:
+            raise Exception("Can't merge information from a tag with only one element (e.g. one sample ; don't use -m option)")
+        
         if merged_col_name in view:
             i_col = view[merged_col_name]
         else:

python/obitools3/dms/view/view.pyx

@@ -7,6 +7,7 @@ cdef dict __VIEW_CLASS__= {}
 from libc.stdlib  cimport malloc
 
 from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.version import version
 
 from ..capi.obiview cimport Alias_column_pair_p, \
                             obi_new_view, \
@@ -183,9 +184,15 @@ cdef class View(OBIWrapper) :
     
     
     @OBIWrapper.checkIsActive
-    def __repr__(self) :         
+    def __repr__(self) :
-        cdef str s = "#View name:\n{name:s}\n#Line count:\n{line_count:d}\n#Columns:\n".format(name       = bytes2str(self.name),
+        cdef str s
-                                                                                                                         line_count = self.line_count)
+        if self.read_only:   # can read date   
+            s = "#View name:\n{name:s}\n#Date created:\n{date:s}\n#Line count:\n{line_count:d}\n#Columns:\n".format(name       = bytes2str(self.name),
+                                                                                                                    line_count = self.line_count,
+                                                                                                                    date       = str(bytes2str_object(self.comments["Date created"])))        
+        else:
+            s = "#View name:\n{name:s}\n#Line count:\n{line_count:d}\n#Columns:\n".format(name       = bytes2str(self.name),
+                                                                                          line_count = self.line_count)
         for column_name in self.keys() :
             s = s + repr(self[column_name]) + '\n'
         return s
@@ -434,6 +441,7 @@ cdef class View(OBIWrapper) :
             for i in range(len(input_view_name)):
                 input_str.append(tostr(input_dms_name[i])+"/"+tostr(input_view_name[i]))
         comments["input_str"] = input_str
+        comments["version"] = version
         return bytes2str_object(comments)
 
     

python/obitools3/format/tab.pyx

@@ -5,6 +5,7 @@ from obitools3.dms.view.view cimport Line
 from obitools3.utils cimport bytes2str_object, str2bytes, tobytes
 from obitools3.dms.column.column cimport Column_line, Column_multi_elts
 
+import sys
 
 cdef class TabFormat:
     
@@ -26,18 +27,22 @@ cdef class TabFormat:
             
             if self.header and self.first_line:
                 if isinstance(data.view[k], Column_multi_elts):
-                    for k2 in data.view[k].keys():
+                    keys = data.view[k].keys()
+                    keys.sort()
+                    for k2 in keys:
                         line.append(tobytes(k)+b':'+tobytes(k2))
                 else:
                     line.append(tobytes(k))
             else:
                 value = data[k]
                 if isinstance(data.view[k], Column_multi_elts):
+                    keys = data.view[k].keys()
+                    keys.sort()
                     if value is None:  # all keys at None
-                        for k2 in data.view[k].keys(): # TODO could be much more efficient
+                        for k2 in keys: # TODO could be much more efficient
                             line.append(self.NAString)
                     else:
-                        for k2 in data.view[k].keys(): # TODO could be much more efficient
+                        for k2 in keys: # TODO could be much more efficient
                             if value[k2] is not None:
                                 line.append(str2bytes(str(bytes2str_object(value[k2]))))  # genius programming
                             else:

python/obitools3/libalign/_solexapairend.pyx

@@ -259,7 +259,7 @@ def buildJoinedSequence(ali, reverse, seq, forward=None):
     seq[b"pairedend_limit"]=len(forward)
     seq[b"seq_length"] = ali.consensus_len
     seq[b"overlap_length"] = ali.overlap_len
-    if ali.consensus_len > 0:
+    if ali.overlap_len > 0:
         seq[b'score_norm']=round(float(ali.score)/ali.overlap_len, 3)
     else:
         seq[b"score_norm"]=0.0

python/obitools3/uri/decode.pyx

@@ -276,11 +276,11 @@ def open_uri(uri,
             iseq = urib
             objclass = bytes
     else:  # TODO update uopen to be able to write? 
-        if urip.path == b'-':
+        if not urip.path or urip.path == b'-':
             file = sys.stdout.buffer
-        elif urip.path :
+        else:
             file = open(urip.path, 'wb')
-        
+
     if file is not None:
         qualifiers=parse_qs(urip.query)
         

python/obitools3/utils.pxd

@@ -2,7 +2,7 @@
 
 from obitools3.dms.capi.obitypes cimport obitype_t, index_t
 
-cpdef bytes format_separator(bytes format)
+cpdef bytes format_uniq_pattern(bytes format)
 cpdef int count_entries(file, bytes format)
 
 cdef obi_errno_to_exception(index_t line_nb=*, object elt_id=*, str error_message=*)

python/obitools3/utils.pyx

@@ -24,11 +24,11 @@ import glob
 import gzip
 
 
-cpdef bytes format_separator(bytes format):
+cpdef bytes format_uniq_pattern(bytes format):
     if format == b"fasta":
         return b"\n>"
     elif format == b"fastq":
-        return b"\n@"
+        return b"\n\+\n"
     elif format == b"ngsfilter" or format == b"tabular":
         return b"\n"
     elif format == b"genbank" or format == b"embl":
@@ -42,7 +42,7 @@ cpdef bytes format_separator(bytes format):
 cpdef int count_entries(file, bytes format):
     
     try:
-        sep = format_separator(format)
+        sep = format_uniq_pattern(format)
         if sep is None:
             return -1
         sep = re.compile(sep)
@@ -72,7 +72,7 @@ cpdef int count_entries(file, bytes format):
                 return -1
             mmapped_file = mmap.mmap(f.fileno(), 0, access=mmap.ACCESS_READ)
             total_count += len(re.findall(sep, mmapped_file))
-            if format != b"ngsfilter" and format != b"tabular" and format != b"embl" and format != b"genbank":
+            if format != b"ngsfilter" and format != b"tabular" and format != b"embl" and format != b"genbank" and format != b"fastq":
                 total_count += 1 # adding +1 for 1st entry because separators include \n (ngsfilter and tabular already count one more because of last \n)
             
     except:

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0b29'
+serial= '0b33'
 
 version ="%d.%d.%s" % (major,minor,serial)

src/obidmscolumn.c

@@ -1725,16 +1725,32 @@ int obi_close_column(OBIDMS_column_p column)
 int obi_clone_column_indexer(OBIDMS_column_p column)
 {
 	char* new_indexer_name;
+	int i;
 
-	new_indexer_name = obi_build_indexer_name((column->header)->name, (column->header)->version);
+	i=0;
-	if (new_indexer_name == NULL)
+	while (true) // find avl name not already used
-		return -1;
-
-	column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
-	if (column->indexer == NULL)
 	{
-		obidebug(1, "\nError cloning a column's indexer to make it writable");
+		new_indexer_name = obi_build_indexer_name((column->header)->name, ((column->header)->version)+i);
-		return -1;
+		if (new_indexer_name == NULL)
+			return -1;
+
+		column->indexer = obi_clone_indexer(column->indexer, new_indexer_name);	// TODO Need to lock this somehow?
+		if (column->indexer == NULL)
+		{
+			if (errno == EEXIST)
+			{
+				free(new_indexer_name);
+				i++;
+			}
+			else
+			{
+				free(new_indexer_name);
+				obidebug(1, "\nError cloning a column's indexer to make it writable");
+				return -1;
+			}
+		}
+		else
+			break;
 	}
 
 	strcpy((column->header)->indexer_name, new_indexer_name);
@@ -2415,16 +2431,20 @@ char* obi_get_formatted_elements_names(OBIDMS_column_p column)
 }
 
 
-char* obi_column_formatted_infos(OBIDMS_column_p column)
+char* obi_column_formatted_infos(OBIDMS_column_p column, bool detailed)
 {
-	char* column_infos;
+	char* column_infos = NULL;
-	char* elt_names;
+	char* elt_names = NULL;
-
+	char* column_name = NULL;
-	column_infos = malloc(1024 * sizeof(char));
+	 // should be in view.c because alias exists in the context of view
+	column_infos = malloc(2048 * sizeof(char)); // TODO
 
 	elt_names = obi_get_formatted_elements_names(column);
 
 
+//  "column_name, data type: OBI_TYPE, element names: [formatted element names](, all comments)"
+
+
 	free(elt_names);
 	return column_infos;
 }