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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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58
python/obitools3/commands/grep.pyx
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@ -7,7 +7,7 @@ from obitools3.uri.decode import open_uri
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
from obitools3.dms.view import RollbackException
from obitools3.apps.config import logger
from obitools3.utils cimport tobytes
from obitools3.utils cimport tobytes, str2bytes
from functools import reduce
import time
@ -267,19 +267,28 @@ 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]
# 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
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_final = output[1]
o_view_name = o_view_name_final
# If the input and output DMS are not the same, create output view in input DMS first, then export it
# to output DMS, making sure the temporary view name is unique in the input DMS
if i_dms != o_dms:
i=0
while o_view_name in i_dms:
o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
i+=1
if "taxoURI" in config["obi"] : # TODO default None problem
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")
@ -307,25 +316,32 @@ def run(config):
# Create output view with the line selection
try:
o_view = selection.materialize(output_view_name)
o_view = selection.materialize(o_view_name)
except Exception, e:
raise RollbackException("obi grep error, rollbacking view: "+str(e), o_view)
# TODO DISCUSS if output URI to different DMS, copy 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])
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
o_view.write_config(config, "grep", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
input[0].record_command_line(command_line) # TODO assuming input and output dms are the same
o_dms.record_command_line(command_line)
# If input and output DMS are not the same, export the temporary view to the output DMS
# and delete the temporary view in the input DMS
if i_dms != o_dms:
o_view.close()
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
o_view = o_dms[o_view_name_final]
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(i_dms, o_view_name)
o_dms.close()
i_dms.close()