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

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This commit is contained in:
Celine Mercier
2016-09-22 18:05:07 +02:00
parent b083745f56
commit b408a4f6eb
6 changed files with 43 additions and 23 deletions
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26
python/obitools3/commands/test.pyx
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@ -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,
@ -333,6 +347,8 @@ 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)

4
src/obiavl.h
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@ -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.
*/

8
src/obidms.h
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@ -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.
*/

2
src/obidmscolumn.h
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@ -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.
*/

22
src/obiview.c
View File

@ -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

2
src/obiview.h
View File

@ -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.
*/