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get _set_vdbcfg worked with file caching turned off #3

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get _set_vdbcfg worked with file caching turned off #3

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106 changes: 55 additions & 51 deletions kmunity/Kmunity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,7 @@ def __init__(self, srr=None, db="mammals", workdir="/tmp", repo="./kmunity", **k
# config setup only
if kwargs.get("config"):
self._get_binary()
self._vdb_config()
# self._vdb_config()

# run checks on existing results, paths and binaries.
else:
Expand Down Expand Up @@ -248,6 +248,7 @@ def _get_binary(self):
self.binaries["prefetch"] = bin_pre
self.binaries["fasterq-dump"] = bin_fas
self.binaries["vdb-config"] = bin_vdb
self._set_vdbcfg()

# print software versions
logger.warning("VERSIONS")
Expand Down Expand Up @@ -458,26 +459,26 @@ def _x_kmerfreq(self, version_only=False):



def _vdb_config(self):
"""
Check whether vdb has been config'd. If not, warn user and exit.
Check whether vdb-config has cache true, and exit if yes.
"""
# user config file is F&$&*$# FORCED to be in home by sra-tools.
logger.warning("CONFIG")
logger.info(
"To finish config sra-tools *requires* you run vdb-config once.")
logger.info(
"I highly recommend turning off 'enable local file caching'.")
logger.info(
"{} -i"
.format(self.binaries["vdb-config"]))
logger.debug(
"This will create a sra-tools config file in {}"
.format(os.path.expanduser("~/.ncbi/")))

logger.debug("")
# user config file is F&$&*$# FORCED to be in home by sra-tools.
# def _vdb_config(self):
# """
# Check whether vdb has been config'd. If not, warn user and exit.
# Check whether vdb-config has cache true, and exit if yes.
# """
# # user config file is F&$&*$# FORCED to be in home by sra-tools.
# logger.warning("CONFIG")
# logger.info(
# "To finish config sra-tools *requires* you run vdb-config once.")
# logger.info(
# "I highly recommend turning off 'enable local file caching'.")
# logger.info(
# "{} -i"
# .format(self.binaries["vdb-config"]))
# logger.debug(
# "This will create a sra-tools config file in {}"
# .format(os.path.expanduser("~/.ncbi/")))
#
# logger.debug("")
# # user config file is F&$&*$# FORCED to be in home by sra-tools.



Expand Down Expand Up @@ -623,36 +624,39 @@ def _clean_work(self):

# THIS DOESN'T WORK, VDB-CONFIG CANNOT DISABLE CACHE NON-INTERACTIVELY
# AS FAR AS I CAN TELL. UGH. NEED TO ASK USERS TO DO IT WITH -I.
# def _set_vdbcfg(self, reset=False):
# # reset to initial value
# if reset:
# cmd0 = [
# "vdb-config", "--set", "cache-disabled:{}"
# .format(self.init_cache)]
# out = sps.Popen(cmd0).communicate()
# logger.debug(
# "{vdb-config} --set cache-disabled:{}"
# .format(self.init_cache))

# # get and store the initial cache setting
# cmd0 = [self.binaries["vdb-config"], "-a"]
# cmd1 = ["grep", "cache"]
# proc0 = sps.Popen(cmd0, stderr=sps.STDOUT, stdout=sps.PIPE)
# proc1 = sps.Popen(cmd1, stdin=proc0.stdout, stdout=sps.PIPE)
# out = proc1.communicate()
# if proc1.returncode:
# logger.error("Failed: {}".format(out[0].decode()))
# raise OSError("Failed: {}".format(out[0].decode()))
# self.init_cache = out[0].decode().split(">")[-1].split("<")[0]

# # set new cache value to "true"
# if self.init_cache != "true":
# cmd0 = [
# self.binaries["vdb-config"], "--set", "cache-disabled:true"]
# out = sps.Popen(cmd0).communicate()
# logger.debug("vdb-config 'cache-disabled' set to 'true'")


def _set_vdbcfg(self, reset=False):
# only "--interactive-mode graphical" works for initialization
if not os.path.exists("~/.ncbi/user-settings.mkfg"):
cmd = [self.binaries["vdb-config"], "-i"]
proc = sps.Popen(cmd, stdin=sps.PIPE, stderr=sps.PIPE, stdout=sps.PIPE)
proc.wait()

# # reset to initial value
# if reset:
# cmd0 = [
# "vdb-config", "--set", "cache-disabled:{}"
# .format(self.init_cache)]
# out = sps.Popen(cmd0).communicate()
# logger.debug(
# "{vdb-config} --set cache-disabled:{}"
# .format(self.init_cache))

# get and store the initial cache setting
# cmd0 = [self.binaries["vdb-config"], "-a"]
# cmd1 = ["grep", "cache"]
# proc0 = sps.Popen(cmd0, stderr=sps.STDOUT, stdout=sps.PIPE)
# proc1 = sps.Popen(cmd1, stdin=proc0.stdout, stdout=sps.PIPE)
# out = proc1.communicate()
# if proc1.returncode:
# logger.error("Failed: {}".format(out[0].decode()))
# raise OSError("Failed: {}".format(out[0].decode()))
# self.init_cache = out[0].decode().split(">")[-1].split("<")[0]

# set new cache value to "true"
cmd0 = [
self.binaries["vdb-config"], "--set", "/repository/user/main/public/cache-disabled=true"]
out = sps.Popen(cmd0).communicate()
logger.debug("vdb-config 'cache-disabled' set to 'true'")



Expand Down