New command: obi sort

python/obitools3/commands/sort.pyx

@@ -0,0 +1,114 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyInputOption, addMinimalOutputOption
+from obitools3.dms.view import RollbackException
+from functools import reduce
+from obitools3.apps.config import logger
+from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
+                                         OBI_CHAR, \
+                                         OBI_FLOAT, \
+                                         OBI_INT, \
+                                         OBI_QUAL, \
+                                         OBI_SEQ, \
+                                         OBI_STR, \
+                                         OBIBool_NA, \
+                                         OBIChar_NA, \
+                                         OBIFloat_NA, \
+                                         OBIInt_NA
+
+import time
+ 
+ 
+NULL_VALUE = {OBI_BOOL: OBIBool_NA, 
+              OBI_CHAR: OBIChar_NA, 
+              OBI_FLOAT: OBIFloat_NA,
+              OBI_INT: OBIInt_NA,
+              OBI_QUAL: [],
+              OBI_SEQ: b"",
+              OBI_STR: b""}
+ 
+
+__title__="Sort view lines according to the value of a given attribute."
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+
+    group=parser.add_argument_group('obi sort specific options')
+
+    group.add_argument('--key', '-k',
+                       action="append", dest="sort:keys",
+                       metavar='<TAG NAME>',
+                       default=[],
+                       type=str,
+                       help="Attribute used to sort the sequence records.")
+
+    group.add_argument('--reverse', '-r',
+                       action="store_true", dest="sort:reverse",
+                       default=False,
+                       help="Sort in reverse order.")
+
+
+def line_cmp(line, key, pb): 
+    pb   
+    if line[key] is None:
+        return NULL_VALUE[line.view[key].data_type_int]
+    else:
+        return line[key]
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi sort")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_view = input[1]
+
+    # Read the name of the output view
+    uri = config['obi']['outputURI'].split('/')
+    if len(uri)==2:
+        # Check that input and output DMS are the same (predicate, to discuss)
+        if config['obi']['inputURI'].split('/')[0] != uri[0]:
+            raise Exception("Input and output DMS must be the same")
+        output_view_name = uri[1]
+    else:
+        output_view_name = uri[0]
+
+    # Initialize the progress bar
+    pb = ProgressBar(len(i_view), config, seconde=5) # TODO
+    
+    keys = config['sort']['keys']
+        
+    selection = Line_selection(i_view)
+    
+    for i in range(len(i_view)):  # TODO special function?
+        selection.append(i)
+    
+    for k in keys:  # TODO order?
+        selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
+
+    # Create output view with the sorted line selection
+    try:
+        o_view = selection.materialize(output_view_name, comments="obi sort: "+str(config['sort']['keys'])+"\n")
+    except Exception, e:
+        raise RollbackException("obi sort error, rollbacking view: "+str(e), o_view)
+
+    # TODO DISCUSS if output URI to different DMS, copy view?
+
+    print("\n")
+    print(repr(o_view))
+
+    input[0].close()
+    #output[0].close()
+