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Author SHA1 Message Date
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 1ae634d56b Added atexit command to obi import, obi uniq and obi less 2017-10-16 11:09:55 +02:00
Celine Mercier 04e065094a All DMS opened by a program are now listed and closed with atexit system 2017-10-16 10:35:07 +02:00
Celine Mercier 5ddd1d9ae6 obi uniq: added taxonomy handling 2017-10-04 16:13:07 +02:00
Celine Mercier 9fc6868341 Increased maximum length for elements names 2017-10-04 16:10:53 +02:00
Celine Mercier f2ece573ff Removed deprecated command 2017-10-04 16:09:41 +02:00
Celine Mercier fb9b219abe Fixed a bug with taxonomy URIs not being read correctly 2017-10-04 16:00:30 +02:00
Celine Mercier 09a5f89849 Column API: improvements to be more flexible when referring to elements 
in columns with several elements per line.
 2017-10-04 15:59:23 +02:00
Celine Mercier 535692b020 Taxonomy: new functions and improvements 2017-10-04 15:55:13 +02:00
Celine Mercier 0ab081f79e Updated obi test to work with changes in taxonomy API 2017-10-04 15:50:32 +02:00
Celine Mercier 1cb05de7e3 Basic obi less 2017-10-04 15:46:26 +02:00
Celine Mercier 532d8e9cd7 obi import: small efficiency improvement when dealing with NA values 2017-10-04 15:44:48 +02:00
Celine Mercier b4088a7928 Cython API: Added basic taxonomy option 2017-10-04 15:42:17 +02:00
Celine Mercier ae24a807da obi uniq: added the option to merge ids, except it only works on small 
sets until lists are implemented properly using obiblobs
 2017-09-25 17:28:03 +02:00
Celine Mercier 75c15594c4 obi uniq: added option to use categories additionally to the sequence to 
determine uniqueness
 2017-09-25 10:56:43 +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 41dec03448 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2017-09-18 16:08:31 +02:00
Celine Mercier 7c57bd33e5 Added check to prevent views from having the name 'taxonomy' (used for 
URIs)
 2017-09-15 14:54:55 +02:00
coissac a776e46e6d Add the command name in the log 2017-09-15 14:51:13 +02:00
Celine Mercier 0e140df0fb Cython API: added some imports in __init__ files 2017-09-14 18:30:04 +02:00
coissac 4bb071c048 Merge branch 'master' of 
git@git.metabarcoding.org:obitools/obitools3.git

Conflicts:
	python/obitools3/commands/import.pyx
 2017-09-05 08:59:45 +02:00
coissac 5045d0c2e9 xxx 2017-09-05 08:58:07 +02:00
Celine Mercier 73bca6288f New obi uniq 2017-08-20 18:04:21 +02:00
Celine Mercier 6a2759eee6 obi import with new input/ouput API 2017-08-20 17:58:36 +02:00
Celine Mercier 38029b1f77 Forgot a ; 2017-08-20 17:56:18 +02:00
Celine Mercier 663a1a1091 Cython API: column elements: added possibility to check if an element 
exists from its index, and a dict-like get() method
 2017-08-20 17:44:05 +02:00
Celine Mercier c6d5436a58 Cython API: fixed a bug where iteration on a NUC_SEQS view would not be 
done correctly (bug appeared with optimization modifications done
lately)
 2017-08-20 17:41:41 +02:00
Celine Mercier 47cad285d6 Cython API: fixed 2 little bugs in Seq API 2017-08-20 17:39:30 +02:00
Celine Mercier 74f15d1a23 Cython API: Various fixes in input handlers (parsers, openers etc). 
Mostly working but not bug-free
 2017-08-20 17:37:51 +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 93cff94e7f Fixed some compilation warnings 2017-08-20 17:25:58 +02:00
Celine Mercier 9744a48a67 BUG FIX: seemingly identical obiblobs would have different hash values 
because of the padding added by the compiler. Fixed by using calloc
instead of malloc for obiblob memory allocation.
 2017-08-20 17:25:15 +02:00
Celine Mercier 6afdc9fb5f AVLs: Added an error check 2017-08-20 17:21:06 +02:00
Celine Mercier 6f202363f4 Fixed a typo in doc 2017-08-20 17:20:13 +02:00
Celine Mercier 7f1ff49aa2 Cython API to import a column and a view from a DMS to another DMS 2017-08-03 16:34:02 +02:00
Celine Mercier 4b86aa67a8 New C functions to import a column and a view from a DMS to another DMS 2017-08-03 16:33:12 +02:00
Celine Mercier a3e81930c2 Views: finished handling and documenting the conditions for an existing 
column to be added to a view
 2017-08-03 16:32:22 +02:00
Celine Mercier 644b55b49f Fixed doc typo 2017-08-03 16:29:25 +02:00
Celine Mercier 927c684fc2 Utils: new function to copy the content of a file into another file 2017-08-03 16:28:54 +02:00
Celine Mercier 344566d9e9 AVLs: made some functions public and changed some rights to be able to 
import AVLs from a DMS to another
 2017-08-03 16:27:43 +02:00
coissac 407f61a408 Add the possibility to create temporary objects like a temporary 
directory and a temporary DMS
 2017-07-28 16:33:19 +02:00
coissac 09ddd74652 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2017-07-28 15:57:01 +02:00
coissac 7c0d882bc9 Patch a bug when creating a DMS not in the current directory. Use the 
basename function to locate the DMS name instead of the loop...
 2017-07-28 15:56:21 +02:00
Celine Mercier 35b0c55a8c Cython API: various improvements and checks 2017-07-28 13:15:13 +02:00
coissac b9c65a871f Patch decoding of URL 2017-07-28 12:41:28 +02:00
Celine Mercier 84bb93096f Cython API: fixes and improvements in Column API 2017-07-28 10:27:04 +02:00
Celine Mercier 01c69e7e25 Cython API: fixed a bug when printing a column 2017-07-28 10:01:56 +02:00
Celine Mercier adf5cbef97 Added DMS method to create a DMS if it doesn't already exists, otherwise 
opens it
 2017-07-28 09:55:43 +02:00
coissac da48a9d1af Patch group of option : types must be callable not a string 2017-07-28 09:36:18 +02:00
Celine Mercier 9482c663c0 minor comments and changes 2017-07-27 19:46:34 +02:00