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ecotag: now closing all DMS properly

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Celine Mercier
2020-04-05 13:20:49 +02:00
parent 0b4a234671
commit 8019dee68e
3 changed files with 13 additions and 10 deletions
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12
python/obitools3/commands/ecotag.pyx
View File

@ -64,10 +64,10 @@ def run(config):
ref_view_name = ref[1] ref_view_name = ref[1]
# Check that the threshold demanded is greater than or equal to the threshold used to build the reference database # Check that the threshold demanded is greater than or equal to the threshold used to build the reference database
if config['ecotag']['threshold'] < eval(i_dms[ref_view_name].comments["ref_db_threshold"]) : if config['ecotag']['threshold'] < eval(ref_dms[ref_view_name].comments["ref_db_threshold"]) :
print("Error: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f).", print("Error: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f).",
config['ecotag']['threshold'], i_dms[ref_view_name].comments["ref_db_threshold"]) config['ecotag']['threshold'], ref_dms[ref_view_name].comments["ref_db_threshold"])
# Open the output: only the DMS # Open the output: only the DMS
output = open_uri(config['obi']['outputURI'], output = open_uri(config['obi']['outputURI'],
input=False, input=False,
@ -126,9 +126,11 @@ def run(config):
# If the input and the output DMS are different, delete the temporary result view in the input DMS # If the input and the output DMS are different, delete the temporary result view in the input DMS
if i_dms != o_dms: if i_dms != o_dms:
View.delete_view(i_dms, o_view_name) View.delete_view(i_dms, o_view_name)
o_dms.close() o_dms.close(force=True)
i_dms.close() taxo_dms.close(force=True)
ref_dms.close(force=True)
i_dms.close(force=True)
logger("info", "Done.") logger("info", "Done.")

9
python/obitools3/dms/dms.pyx
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@ -94,16 +94,16 @@ cdef class DMS(OBIWrapper):
return dms return dms
def close(self) : def close(self, force=False) :
''' '''
Closes the DMS instance and free the associated memory Closes the DMS instance and free the associated memory (no counter, closing is final)
The `close` method is automatically called by the object destructor. The `close` method is automatically called by the object destructor.
''' '''
cdef OBIDMS_p pointer = self.pointer() cdef OBIDMS_p pointer = self.pointer()
if self.active() : if self.active() :
OBIWrapper.close(self) OBIWrapper.close(self)
if (obi_close_dms(pointer, False)) < 0 : if (obi_close_dms(pointer, force=force)) < 0 :
raise Exception("Problem closing an OBIDMS") raise Exception("Problem closing an OBIDMS")
@ -254,7 +254,8 @@ cdef class DMS(OBIWrapper):
# bash command history property getter # bash command history property getter
@property @property
def bash_history(self): def bash_history(self):
s = b"#!/bin/bash\n\n" #s = b"#!${bash}/bin/bash\n\n"
s = b""
first = True first = True
for command in self.command_line_history: for command in self.command_line_history:
s+=b"#" s+=b"#"

2
python/obitools3/version.py
View File

@ -1,5 +1,5 @@
major = 3 major = 3
minor = 0 minor = 0
serial= '0-beta11' serial= '0-beta12a'
version ="%d.%02d.%s" % (major,minor,serial) version ="%d.%02d.%s" % (major,minor,serial)