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121 Commits

Author SHA1 Message Date
MercierC
7f0f63cf26 C: now completely unmapping files before truncating them to a smaller 
size (#68)
 2021-03-11 15:12:40 +13:00
Celine Mercier
ad1fd3c341 Now handling dictionaries with one key 2021-03-10 16:50:30 +13:00
Celine Mercier
137c109f86 obi ls: now done in C (preparing things for R packages to read DMS) and 
switch to version 3.0.0b36
 2020-09-29 17:51:39 +02:00
Celine Mercier
1da6aac1b8 C: patch for failed creation of AVL with errno EEXIST 2020-08-12 17:55:08 +02:00
Celine Mercier
e28507639a C and Cython: fixed and improved the associated columns system 2020-07-26 17:39:29 +02:00
Celine Mercier
49b8810a76 C: made indexer opening/closing cleaner 2020-06-13 21:47:03 +02:00
Celine Mercier
8776ce22e6 C: fixed a bug where indexers referring to tuples of certain types were 
not properly closed and imported
 2020-06-09 14:34:43 +02:00
Celine Mercier
0f745e0113 C: Columns: optimizing column file growth 2020-04-18 13:55:47 +02:00
Celine Mercier
e9a40630e9 C: Columns: rounding column growth to ceil to avoid looping on small 
values
 2020-04-13 19:02:10 +02:00
Celine Mercier
44517db51f Fixed gcc warnings 2019-09-25 11:38:00 +02:00
Celine Mercier
783a1343c4 DMS are now locked when used by a command. Added checks and changed 
cleaning mechanisms.
 2019-09-20 20:37:19 +02:00
Celine Mercier
5e3c41b058 C: Fixed opened DIR leak 2019-09-04 16:48:13 +02:00
Celine Mercier
a7fabff1c7 C: made it so column DIR* are not kept open to handle very large DMS 2019-09-04 12:55:21 +02:00
Celine Mercier
af7cecf59f Fixed a bug where a directory was not closed properly resulting in errno 
24 sometimes
 2019-08-18 19:46:52 +02:00
Celine Mercier
1ee50b7222 Fixed a bug when creating a column and checking the comments string if 
it was NULL
 2019-03-07 15:09:59 +01:00
Celine Mercier
0b62619e4e Various commentaries and insignificant fixes 2019-01-21 17:32:44 +01:00
Celine Mercier
6b1c41f3fb Changed an error message to be more specific 2018-11-07 13:37:25 +01:00
Celine Mercier
e18b762d81 Weird buggy Eclipse commit with nothing changed 2018-10-21 17:35:18 +02:00
Celine Mercier
bc8c394061 Columns: implemented handling of JSON formatted comments 2018-10-07 18:54:51 +02:00
Celine Mercier
f0c147c252 C API: Added a function to set an entire column to a specified (atomic) 
value.
 2018-05-17 15:59:16 +02:00
Celine Mercier
1fd3323372 Columns: elements names informations are now kept in a memory arena of 
adapted size in the header, and added a boolean in the header indicating
whether the values should be evaluated (typically character strings to
be evaluated in Python)
 2017-12-13 22:46:50 +01:00
Celine Mercier
0998268955 Fixed two little potential bugs when cleaning unfinished columns and 
deleted old trace
 2017-11-24 18:03:59 +01:00
Celine Mercier
3ba7ce1c91 View rollback: version files and column directories aren't deleted 
anymore to prevent indexer bug, and fixed a freeing bug
 2017-11-15 17:27:26 +01:00
Celine Mercier
9a50803c00 Added tuple columns containing immutable indexed data arrays of any type 2017-11-15 13:48:59 +01:00
Celine Mercier
dfd51939a0 Views are now rollbacked if an error occurs, and unfinished views and 
columns are deleted when an OBIDMS is opened.
 2017-10-26 18:58:48 +02:00
Celine Mercier
5ed6835e0e Fixed a bug where the new line count when truncating a column would not 
be computed correctly when dealing with high numbers (bad automatic type
for intermediate result)
 2017-09-25 10:52:19 +02:00
Celine Mercier
c559ddf487 BUG FIX: creation of a new column would fail because of a case not 
handled when a high number of elements per line would imply less than
one line per memory page
 2017-08-20 17:30:23 +02:00
Celine Mercier
c5f3fdc295 Increased maximum element names length in columns 2017-07-27 19:44:49 +02:00
Celine Mercier
59dd0a8a8c Standardized and improved the API to create new columns, updated the doc 2017-07-18 17:34:32 +02:00
Celine Mercier
f5e992abbf Added a check on the element when setting a value in a column 2017-07-05 14:49:20 +02:00
Celine Mercier
431c1c8c6a Merge branch 'Eric_new_Python_API' of 
git@git.metabarcoding.org:obitools/obitools3.git into
Eric_new_Python_API

Conflicts:
	python/obitools3/obidms/_obidms.pxd
	python/obitools3/obidms/_obidms.pyx
	python/obitools3/obidms/_obidmscolumn_bool.pyx
	python/obitools3/obidms/_obidmscolumn_str.pyx
	python/obitools3/obidms/_obiseq.pxd
	python/obitools3/obidms/_obiseq.pyx
	python/obitools3/obidms/_obitaxo.pxd
	python/obitools3/obidms/_obitaxo.pyx
	python/obitools3/obidms/_obiview.pxd
	python/obitools3/obidms/_obiview.pyx
	python/obitools3/obidms/_obiview_nuc_seq.pxd
	python/obitools3/obidms/_obiview_nuc_seq.pyx
	python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
	python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
	python/obitools3/obidms/capi/obialign.pxd
	python/obitools3/obidms/capi/obidmscolumn.pxd
	python/obitools3/obidms/capi/obitaxonomy.pxd
	python/obitools3/obidms/capi/obiview.pxd
 2017-02-20 14:55:36 +01:00
Celine Mercier
e50da64ea1 The elements names when a column contains several elements per line are 
now formatted with '\0' as separator and handled in a more optimized way
 2017-01-31 16:48:06 +01:00
Eric Coissac
daacd0df76 Strong refactoring 1 2016-12-26 13:35:31 +01:00
Celine Mercier
936be64c34 Goes with 5e0c9f87 (missing ';' and fixed compilation warnings) 2016-12-05 11:18:29 +01:00
Celine Mercier
5e0c9f878b Added the doc for the function building the element names, and a missing 
free
 2016-12-05 10:46:21 +01:00
Celine Mercier
852e5488c8 The default element names for columns with multiple elements per line 
are now "O;1;2;...;n"
 2016-12-02 17:54:51 +01:00
Celine Mercier
7d022c1a52 If the indexer name is NULL when creating a column, it now becomes the 
column name
 2016-11-18 15:56:51 +01:00
Celine Mercier
8f724f4f8e Some code refactoring 2016-11-09 16:48:00 +01:00
Celine Mercier
43f3c69a40 Fixed bug when cloning column with line selection 2016-09-21 17:50:21 +02:00
Celine Mercier
a0da984003 Fixed bug where columns would not get truncated to the right size, and 
fixed bug where column directories would be open and not closed in some
instances
 2016-09-21 17:28:52 +02:00
Celine Mercier
986f90c59e Fixed bug where column directories weren't closed correctly, leading to 
too many file descriptors open, and added error checking when closing
file descriptors
 2016-09-15 12:18:40 +02:00
Celine Mercier
2d8ac2b035 Fixed bug when creating an OBI_IDX column 2016-08-11 17:30:32 +02:00
Celine Mercier
38718320f9 First version for the association of one column to another. Closes #55 2016-07-15 15:38:49 +02:00
Celine Mercier
799b942017 Deleted old debugging print 2016-06-03 18:57:32 +02:00
Celine Mercier
e681ca646d Fixed a problem with some columns being shorter in views and triggering 
errors when trying to get values. Temporary fix that needs discussion
 2016-05-20 18:45:29 +02:00
Celine Mercier
8ae7644945 First version of quality handling (not working yet) and now it is 
checked that a column is writable before enlarging it
 2016-05-11 16:38:14 +02:00
Celine Mercier
f3b20b809d Fixed bug with indexer names being defined and generating seg fault if 
creating a column not using indexers
 2016-04-27 14:01:36 +02:00
Celine Mercier
66045acf1d Creating a column now uses the function to create the indexer name if 
one was not provided
 2016-04-22 17:47:00 +02:00
Celine Mercier
ffa4557928 changed MAP_PRIVATE flags to MAP_SHARED when opening a column because it 
seems a lot more efficient
 2016-04-22 16:26:24 +02:00
Celine Mercier
003cd11362 Fixed initialization of NA values for OBI_STR and OBI_SEQ columns 2016-04-22 16:14:23 +02:00