Updated obi test to test NUC_SEQS views and the taxonomy API

python/obitools3/commands/test.pyx

@@ -1,7 +1,9 @@
 from obitools3.apps.progress cimport ProgressBar  # TODO I absolutely don't understand why it doesn't work without that line
 from obitools3.dms.view.view import View, Line_selection
+from obitools3.dms.view.typed_view.view_NUC_SEQS import View_NUC_SEQS
 from obitools3.dms.dms import DMS
 from obitools3.dms.column import Column
+from obitools3.dms.taxo.taxo import OBI_Taxonomy
 from obitools3.utils cimport str2bytes
  
 import shutil
@@ -9,7 +11,7 @@ import string
 import random
  
  
-VIEW_TYPES = [""] #, "NUC_SEQS_VIEW"]
+VIEW_TYPES = ["", "NUC_SEQS_VIEW"]
 #COL_TYPES = ["OBI_BOOL", "OBI_CHAR", "OBI_FLOAT", "OBI_INT", "OBI_SEQ", "OBI_STR"]
 COL_TYPES = [1, 2, 3, 4, 6, 7]
 NUC_SEQUENCE_COLUMN = "NUC_SEQ"
@@ -17,7 +19,9 @@ ID_COLUMN = "ID"
 DEFINITION_COLUMN = "DEFINITION"
 QUALITY_COLUMN = "QUALITY"    
 SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
- 
+
+#TAXDUMP = "" TODO path=?
+TAXTEST = "taxtest"
  
 NAME_MAX_LEN = 200
 COL_COMMENTS_MAX_LEN = 2048
@@ -25,40 +29,61 @@ MAX_INT = 2147483647    # used to generate random float values
  
  
 __title__="Tests if the obitools are working properly"
- 
+
- 
+
 default_config = {   
                  }
- 
+
- 
+
+
+def test_taxo(config, infos):
+    tax1 = OBI_Taxonomy.open(infos['dms'], config['obi']['taxo'], taxdump=True)
+    tax1.write(TAXTEST)
+    tax2 = OBI_Taxonomy.open(infos['dms'], TAXTEST, taxdump=False)
+    assert len(tax1) == len(tax2), "Length of written taxonomy != length of read taxdump : "+str(len(tax2))+" != "+str(len(tax1))
+    
+    i = 0
+    for x in range(config['test']['nbtests']):
+        idx = random.randint(0, len(tax1)-1)
+        t1 = tax1.get_taxon_by_idx(idx)
+        t2 = tax2.get_taxon_by_idx(idx)
+        assert t1 == t2, "Taxon gotten from written taxonomy != taxon read from taxdump : "+str(t2)+" != "+str(t1)
+        i+=1
+        if (i%(config['test']['nbtests']/10)) == 0 :
+            print("Testing taxonomy functions......"+str(i*100/config['test']['nbtests'])+"%")
+
+    tax1.close()
+    tax2.close()
+
+
 def random_length(max_len):
     return random.randint(1, max_len)
- 
+
- 
+
 def random_bool(config):
     return random.choice([True, False])
- 
+
- 
+
 def random_char(config):
     return str2bytes(random.choice(string.ascii_lowercase))
- 
+
- 
+
 def random_float(config):
     return random.randint(0, MAX_INT) + random.random()
-     
+
- 
+
 def random_int(config):
     return random.randint(0, config['test']['maxlinenb'])
- 
+
- 
+
 def random_seq(config):
     return str2bytes(''.join(random.choice(['a','t','g','c']) for i in range(random_length(config['test']['seqmaxlen']))))
- 
+
- 
+
 def random_bytes(config):
     return random_bytes_with_max_len(config['test']['strmaxlen'])
- 
+
- 
+
 def random_str_with_max_len(max_len):
     return ''.join(random.choice(string.ascii_lowercase) for i in range(random_length(max_len)))
 
@@ -245,8 +270,11 @@ def random_new_view(config, infos, first=False):
     elif v_to_clone is not None :
         infos['view'] = v_to_clone.clone(random_unique_name(infos), comments=random_str_with_max_len(config['test']['commentsmaxlen']))
     else :
-        infos['view'] = View.new(infos['dms'], random_unique_name(infos), comments=random_str_with_max_len(config['test']['commentsmaxlen']))   # TODO random view class
+        if v_type == "NUC_SEQS_VIEW" :
-         
+            infos['view'] = View_NUC_SEQS.new(infos['dms'], random_unique_name(infos), comments=random_str_with_max_len(config['test']['commentsmaxlen']))   # TODO quality column
+        else :
+            infos['view'] = View.new(infos['dms'], random_unique_name(infos), comments=random_str_with_max_len(config['test']['commentsmaxlen']))   # TODO quality column
+            
     print_test(config, repr(infos['view']))
     if v_to_clone is not None :
         if line_selection is None:
@@ -280,7 +308,14 @@ def addOptions(parser):
                        type=str,
                        help="Name of the default DMS for reading and writing data. "
                             "Default: /tmp/test_dms")
- 
+    
+    group.add_argument('--taxo','-t', 
+                       action="store", dest="obi:taxo",
+                       metavar='<TAXDUMP PATH>',
+                       type=str,
+                       help="Path to a taxdump to test the taxonomy.")      # TODO
+
+     
     group=parser.add_argument_group('obi test specific options')
  
     group.add_argument('--nb_tests','-n',
@@ -299,7 +334,7 @@ def addOptions(parser):
                        help="Maximum length of DNA sequences. "
                             "Default: 200")
  
-    group.add_argument('--str_max_len','-t',
+    group.add_argument('--str_max_len','-r',
                        action="store", dest="test:strmaxlen",
                        metavar='<STR_MAX_LEN>',
                        default=200,
@@ -370,7 +405,7 @@ def run(config):
     print("Initializing the DMS and the first view...")
      
     shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
- 
+    
     ini_dms_and_first_view(config, infos)
     print_test(config, repr(infos['view']))
      
@@ -383,7 +418,9 @@ def run(config):
             print("Testing......"+str(i*100/config['test']['nbtests'])+"%")
  
     #print(infos)
-     
+    
+    test_taxo(config, infos)
+    
     infos['view'].close()
     infos['dms'].close()
     shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)