Changed file name limits to adapt to system limits + minor changes

python/obitools3/commands/test.pyx

@@ -20,10 +20,8 @@ QUALITY_COLUMN = "QUALITY"
 SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
 
 
-NAME_MAX_LEN = 50
+NAME_MAX_LEN = 200
 COL_COMMENTS_MAX_LEN = 2048
-MAX_NB_ELEMENTS_PER_LINE = 20
-ELEMENT_NAME_MAX_LEN = int(2048 / MAX_NB_ELEMENTS_PER_LINE)
 MAX_INT = 2147483647    # used to generate random float values
 
 
@@ -78,6 +76,14 @@ def random_unique_name(infos):
     return name
 
 
+def random_unique_element_name(config, infos):
+    name = ""
+    while name == "" or name in infos['unique_names'] :
+        name = random_str_with_max_len(config['test']['elt_name_max_len'])
+    infos['unique_names'].append(name)
+    return name
+
+
 def print_test(config, sentence):
     if config['test']['verbose'] :
         print(sentence)
@@ -180,10 +186,10 @@ def fill_column(config, infos, col) :
             
 def create_random_column(config, infos) :
     alias = random.choice(['', random_unique_name(infos)])
-    nb_elements_per_line=random.randint(1, MAX_NB_ELEMENTS_PER_LINE)
+    nb_elements_per_line=random.randint(1, config['test']['maxelts'])
     elements_names = []
     for i in range(nb_elements_per_line) :
-        elements_names.append(random_unique_name(infos))
+        elements_names.append(random_unique_element_name(config, infos))
     name = random_unique_name(infos)
     infos['view'].add_column(name, 
                              alias=alias, 
@@ -317,6 +323,14 @@ def addOptions(parser):
                        help="Maximum number of lines in a column."
                             "Default: 10000")
 
+    group.add_argument('--max_elts_per_line','-e',
+                       action="store", dest="test:maxelts",
+                       metavar='<MAX_ELTS_PER_LINE>',
+                       default=20,
+                       type=int,
+                       help="Maximum number of elements per line in a column."
+                            "Default: 20")
+
     group.add_argument('--verbose','-v',
                        action="store_true", dest="test:verbose",
                        default=False,
@@ -333,8 +347,10 @@ def run(config):
              'tests': [test_set_and_get, test_add_col, test_delete_col, test_col_alias, test_new_view]
             }
 
+    config['test']['elt_name_max_len'] = int((COL_COMMENTS_MAX_LEN - config['test']['maxelts']) / config['test']['maxelts'])
+
     print("Initializing the DMS and the first view...")
-        
+            
     ini_dms_and_first_view(config, infos)
     
     i = 0

src/obiavl.h

@@ -30,7 +30,7 @@
 #include "encode.h"
 
 
-#define MAX_NB_OF_AVLS_IN_GROUP (100)						/**< The maximum number of AVL trees in a group.	// TODO discuss
+#define MAX_NB_OF_AVLS_IN_GROUP (1000)						/**< The maximum number of AVL trees in a group.	// TODO discuss
                               	  	 	 	 	 	 	 	 */
 #define MAX_NODE_COUNT_PER_AVL (10000000)					/**< The maximum number of nodes in an AVL tree.
 															 *   Only used to decide when to create a new AVL in a group, and to initialize the bloom filter // TODO discuss.
@@ -42,7 +42,7 @@
  	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 */
 #define AVL_MAX_DEPTH (1024)								/**< The maximum depth of an AVL tree. Used to save paths through the tree.
                               	  	 	 	 	 	 	 	 */
-#define AVL_MAX_NAME (1024) 								/**< The maximum length of an AVL tree name.
+#define AVL_MAX_NAME (250) 				     				/**< The maximum length of an AVL tree name.
                               	  	 	 	 	 	 	 	 */
 #define AVL_GROWTH_FACTOR (2)								/**< The growth factor when an AVL tree is enlarged.
                                 	 	 	 	 	 	 	 */

src/obidms.h

@@ -26,7 +26,7 @@
 #include "obitypes.h"
 
 
-#define OBIDMS_MAX_NAME (2048) 	    			/**< The maximum length of an OBIDMS name.
+#define OBIDMS_MAX_NAME (247) 	    			/**< The maximum length of an OBIDMS name.
  	 	 	 	 	 	 	 	 	 	 	 	 */
 #define INDEXER_DIR_NAME "OBIBLOB_INDEXERS"  	/**< The name of the Obiblob indexer directory.
                                 	 	 	 	 */
@@ -34,11 +34,11 @@
 												 */
 #define TAXONOMY_DIR_NAME "TAXONOMY"    		/**< The name of the taxonomy directory.
                                 	 	 	 	 */
-#define MAX_NB_OPENED_COLUMNS (100) 			/**< The maximum number of columns open at the same time.
+#define MAX_NB_OPENED_COLUMNS (1000) 			/**< The maximum number of columns open at the same time.
                                 	 	 	 	 */
-#define MAX_NB_OPENED_INDEXERS (100) 			/**< The maximum number of indexers open at the same time.
+#define MAX_NB_OPENED_INDEXERS (1000) 			/**< The maximum number of indexers open at the same time.
                                 	 	 	 	 */
-#define MAX_PATH_LEN 4096						/**< Maximum length for the character string defining a
+#define MAX_PATH_LEN (1024)						/**< Maximum length for the character string defining a
  	 	 	 	 	 	 	 	 	 	 	 	 *	 file or directory path.
  	 	 	 	 	 	 	 	 	 	 	 	 */
 

src/obidmscolumn.h

@@ -28,7 +28,7 @@
 #include "obiblob_indexer.h"
 
 
-#define ELEMENTS_NAMES_MAX (2048)     	/**< The maximum length of the list of elements names.
+#define ELEMENTS_NAMES_MAX (2048)     	/**< The maximum length of the list of elements names.	// TODO Discuss
                                 	     */
 #define COLUMN_GROWTH_FACTOR (2)	 	/**< The growth factor when a column is enlarged.
                                 	   	 */

src/obiview.c

@@ -1645,7 +1645,6 @@ int obi_view_add_column(Obiview_p view,
 	int             			i;
 	OBIDMS_column_p 			column;
 	OBIDMS_column_p 			column_buffer;
-	OBIDMS_column_p 			current_line_selection;
 
 	// Check that the view is not read-only
 	if (view->read_only)
@@ -1702,19 +1701,24 @@ int obi_view_add_column(Obiview_p view,
 	if (create)
 	{	// Create column
 		column = obi_create_column(view->dms, column_name, data_type, nb_lines, nb_elements_per_line, elements_names, indexer_name, associated_column_name, associated_column_version, comments);
+		if (column == NULL)
+		{
+			obidebug(1, "\nError creating a column to add to a view");
+			return -1;
+		}
 		(column->header)->lines_used = nb_lines;
 	}
 	else
 	{ // Open column
-	  // TODO do we require that the column's line count is equal to the view's line count?
-	  //      or do we enlarge the column or the view as needed?
 		column = obi_open_column(view->dms, column_name, version_number);
-	}
-
-	if (column == NULL)
-	{
-		obidebug(1, "\nError creating or opening a column to add to a view");
-		return -1;
+		if (column == NULL)
+		{
+			obidebug(1, "\nError opening a column to add to a view");
+			return -1;
+		}
+		// Check that the column's line count is equal to the view's line count if there is no line selection.
+		// TODO But what if there is a line selection ??? imo should just check that col_line_count > line_selection_count
+		//if ()
 	}
 
 	// Store column pointer in the view structure

src/obiview.h

@@ -28,7 +28,7 @@
 #include "hashtable.h"
 
 
-#define OBIVIEW_NAME_MAX_LENGTH (255)   		/**< The maximum length of an OBIDMS view name.
+#define OBIVIEW_NAME_MAX_LENGTH (249)   		/**< The maximum length of an OBIDMS view name, without the extension.
                                 	 	  	  	 */
 #define VIEW_TYPE_MAX_LENGTH (1024)   			/**< The maximum length of the type name of a view.
                                 	 	  	  	 */