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Commands: updated for JSON formatted comments with history

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This commit is contained in:
Celine Mercier
2018-10-07 19:10:34 +02:00
parent 35cf2962cc
commit e9a41c5b97
11 changed files with 144 additions and 34 deletions
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22
python/obitools3/commands/annotate.pyx
View File

@ -9,16 +9,16 @@ from obitools3.dms.view import RollbackException
from functools import reduce
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
import time
import math
from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
QUALITY_COLUMN, \
COUNT_COLUMN
import time
import math
import sys
__title__="Annotate views with new tags and edit existing annotations"
@ -285,10 +285,10 @@ def run(config):
output_view_name = uri[0]
# Clone output view from input view
o_view = i_view.clone(output_view_name, comments=i_view.comments+b"\nobi annotate") # TODO comments
o_view = i_view.clone(output_view_name, comments=i_view.comments) # TODO comments
if o_view is None:
raise Exception("Couldn't create output view")
if 'taxoURI' in config['obi'] : # TODO default None problem
taxo_uri = open_uri(config['obi']['taxoURI'])
if taxo_uri is None:
@ -341,6 +341,16 @@ def run(config):
except Exception, e:
raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
# Save command config in View and DMS comments
command_line = " ".join(sys.argv[1:])
input_dms_name=[input[0].name]
input_view_name=[input[1].name]
if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
input_dms_name.append(config['obi']['taxoURI'].split("/", 1)[0])
input_view_name.append(config['obi']['taxoURI'].split("/", 1)[1])
o_view.write_config(config, "annotate", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
input[0].record_command_line(command_line) # TODO assuming same dms
print("\n")
print(repr(o_view))