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All commands now handle outputing to another DMS + small fixes

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This commit is contained in:
Celine Mercier
2018-11-02 19:03:09 +01:00
parent 8a8e9e50b2
commit 35f3e7c30b
10 changed files with 266 additions and 153 deletions
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54
python/obitools3/commands/annotate.pyx
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@ -8,7 +8,7 @@ from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption
from obitools3.dms.view import RollbackException
from functools import reduce
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, str2bytes
from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
ID_COLUMN, \
DEFINITION_COLUMN, \
@ -272,24 +272,39 @@ def run(config):
input = open_uri(config['obi']['inputURI'])
if input is None:
raise Exception("Could not read input view")
i_dms = input[0]
i_view = input[1]
i_view_name = input[1].name
# Read the name of the output view
uri = config['obi']['outputURI'].split('/')
if len(uri)==2:
# Check that input and output DMS are the same (predicate, to discuss)
if config['obi']['inputURI'].split('/')[0] != uri[0]:
raise Exception("Input and output DMS must be the same")
output_view_name = uri[1]
else:
output_view_name = uri[0]
# Open the output: only the DMS, as the output view is going to be created by cloning the input view
# (could eventually be done via an open_uri() argument)
output = open_uri(config['obi']['outputURI'],
input=False,
dms_only=True)
if output is None:
raise Exception("Could not create output view")
o_dms = output[0]
o_view_name = output[1]
# If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
# (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
if i_dms != o_dms:
imported_view_name = i_view_name
i=0
while imported_view_name in o_dms: # Making sure view name is unique in output DMS
imported_view_name = i_view_name+b"_"+str2bytes(str(i))
i+=1
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
i_view = o_dms[imported_view_name]
# Clone output view from input view
o_view = i_view.clone(output_view_name, comments=i_view.comments) # TODO comments
o_view = i_view.clone(o_view_name)
if o_view is None:
raise Exception("Couldn't create output view")
i_view.close()
if 'taxoURI' in config['obi'] : # TODO default None problem
# Open taxonomy if there is one
if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
taxo_uri = open_uri(config['obi']['taxoURI'])
if taxo_uri is None:
raise Exception("Couldn't open taxonomy")
@ -345,16 +360,19 @@ def run(config):
# 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]
input_view_name=[i_view_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])
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-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
output[0].record_command_line(command_line)
print("\n")
print(repr(o_view))
input[0].close()
# output[0].close()
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
if i_dms != o_dms:
View.delete_view(o_dms, imported_view_name)
o_dms.close()
i_dms.close()