Add the possibility to create temporary objects like a temporary

directory and a temporary DMS
This commit is contained in:
2017-07-28 16:33:19 +02:00
parent 09ddd74652
commit 407f61a408
7 changed files with 175 additions and 20 deletions

View File

@ -13,6 +13,8 @@ from obitools3.dms.view.view cimport View
from obitools3.dms.view.typed_view.view_NUC_SEQS import View_NUC_SEQS # TODO cimport doesn't work
from obitools3.dms.column.column cimport Column
from obitools3.dms.obiseq import Nuc_Seq
from obitools3.utils cimport tobytes, \
get_obitype, \
update_obitype
@ -25,6 +27,8 @@ from obitools3.dms.capi.obierrno cimport obi_errno
from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption
from obitools3.uri.decode import open_uri
from obitools3.apps.config import logger
__title__="Imports sequences from different formats into a DMS"
@ -76,17 +80,26 @@ def run(config):
cdef list new_elements_names
cdef ProgressBar pb
global obi_errno
logger=config['obi']['logger']
logger.info("obi import : imports file into an DMS")
logger("info","obi import : imports file into an DMS")
inputs = open_uri(config['obi']['inputURI'])
print(inputs)
if inputs[2]==Nuc_Seq:
v = View_NUC_SEQS
else:
v= View
print(v)
output = open_uri(config['obi']['outputURI'],
input=False,
newviewtype=v)
print(input)
print(output)
sys.exit()
# pb = ProgressBar(1000000, config, seconde=5) # TODO should be number of records in file