automatic tar xf of file with unknown name Post: 302125898

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Top Forums UNIX for Dummies Questions & Answers automatic tar xf of file with unknown name Post 302125898 by tkrahn on Monday 9th of July 2007 02:34:59 AM

07-09-2007

Registered User

Thanks very much era!

The curl string was embedded inside a C source code and was hard coded compiled with the application (Hawkeye viewer for Amos, see http://amos.sourceforge.net). The author has used the % signs for replacing string segments by variables with a string function. It has nothing to do with DOS I think.
For this reason the slash was in front of the " to hide it and I forgot to delete it before I posted the thread.

Hawkeye has only space for a single command line, so I decided to put everything into an external script "fetchscf.sh" as you started it already. The command line in Hawkeye is now only

/usr/local/bin/fetchscf.sh %EID% %TRACECACHE%

fetchscf.sh contains:

<source>
#!/bin/sh

EID=$1
tracecache=$2

curl "http://www.ncbi.nlm.nih.gov/Traces/trace.fcgi?cmd=retrieve&save=1&srcf=1&scfrcf=scf&file=trace&val=$EID&ti=$EID" -s -o $tracecache/$EID.tar
tar tvf $tracecache/$EID.tar | grep ' \.scf$' | cut -d: -f2 | cut -b4- | xargs tar xOf $tracecache/$EID.tar >$tracecache/$EID.scf
</source>

Because tar tvf returned the whole info line including the date etc.
-rw-rw-r-- 0/0 106207 2007-07-09 00:29 2007_07_09_01h29m40s/BACILLUS_ANTHRACIS_STR._AMES_0581/TIGR/traces/BAEAT42TR.scf

I had to cut the string from the left side until the first character of the path name.
I wasn't sure if this length was always exactly constant, but I assumed that the time was always separated by ":" and then the fourth byte is the beginning of the path name. This explains the double cut in the pipe.
Maybe this is not perfectly elegant, but it works fine. It isn't worth making it more perfect, because NCBI will change the path names and URL parameters every three month or so.

Thanks again for your help!

Thomas

tkrahn

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bpstats2

BPSTATS2(1)							  BP executables						       BPSTATS2(1)

NAME

       bpstats2 - Bundle Protocol (BP) processing statistics query utility via bundles

SYNOPSIS

       bpstats2 sourceEID [default destEID] [ct]

DESCRIPTION

       bpstats2 creates bundles containing the current values of all BP processing statistics accumulators.  It creates these bundles when:

       o   an interrogation bundle is delivered to sourceEID: the contents of the bundle are discarded, a new statistics bundle is generated and
	   sent to the source of the interrogation bundle.  The format of the interrogation bundle is irrelevant.

       o   a SIGUSR1 signal is delivered to the bpstats2 application: a new statistics bundle is generated and sent to default destEID.

EXIT STATUS

       0   bpstats2 has terminated. Any problems encountered during operation will be noted in the ion.log log file.

       1   bpstats2 failed to start up or receive bundles.  Diagnose the issue reported in the ion.log file and try again.

OPTIONS

       [ct]
	   If the string "ct" is appended as the last argument, then statistics bundles will be sent with custody transfer requested.

FILES

       No configuration files are needed.

ENVIRONMENT

       No environment variables apply.

DIAGNOSTICS

       The following diagnostics may be issued to the ion.log log file:

       bpstats2 can't bp_attach().
	   bpadmin has not yet initialized BP operations.

       bpstats2 can't open own endpoint.
	   Another BP application has opened that endpoint; close it and try again.

       No space for ZCO extent.
	   ION system error.  Check for earlier diagnostic messages describing the cause of the error; correct problem and rerun.

       Can't create ZCO extent.
	   ION system error.  Check for earlier diagnostic messages describing the cause of the error; correct problem and rerun.

       bpstats2 can't send stats bundle.
	   Bundle Protocol service to the remote endpoint has been stopped.

       Can't send stats: bad dest EID (dest EID)
	   The destination EID printed is an invalid destination EID.  The destination EID may be specified in default destEID or the source EID
	   of the interrogation bundle.  Ensure that default destEID is an EID that is valid for ION, and that the interrogator is a source EID
	   that is also a valid destination EID.  Note that "dtn:none" is not a valid destination EID, but is a valid source EID.

NOTES

       A very simple interrogator is bpchat which can repeatedly interrogate bpstats2 by just striking the enter key.

BUGS

       Report bugs to <ion-bugs@korgano.eecs.ohiou.edu>

SEE ALSO

       bpstats(1), bpchat(1)

perl v5.14.2							    2012-05-25							       BPSTATS2(1)