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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
|
|
407f61a408
|
Add the possibility to create temporary objects like a temporary
directory and a temporary DMS
|
2017-07-28 16:33:19 +02:00 |
|
|
|
09ddd74652
|
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
|
2017-07-28 15:57:01 +02:00 |
|
|
|
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 |
|
|
|
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 |
|
|
|
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 |
|
