In this thread: /shell-programming-and-scripting/255687-organizing-text-file-capital-names-capital-word-capital-word.html (sorry i cant use links)
that is not an example, those are real students names with real student login id's for the college i am attending and i am on that list. Please... (3 Replies)
Discussion started by: throwawayacc
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Hi
Kindly remove the following from the post . These are confidential info posted by mistake
https://www.unix.com/shell-programming-and-scripting/201037-perl-while-loop-each.html
please remove the comments section which is first 16 lines in the perl script .
Also please remove the ... (1 Reply)
Discussion started by: ptappeta
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Hi Sir,
please remove following terms from post as it is sensitive data
https://www.unix.com/shell-programming-and-scripting/235655-print-single-line.html
ifeeds
fidedev
ironsides
feedmgr
thanks a lot
prabhu (1 Reply)
Discussion started by: ptappeta
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HI Sir ,
please remove the sensitive data from the post
https://www.unix.com/unix-for-advanced-and-expert-users/200219-ssh-issue.html
please blank the following terms
/home/infafi/Informatica/PowerCenter8.1.1/server/bin
iminfu01uat
... (4 Replies)
Discussion started by: ptappeta
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Hello,
Can you please delete or modify a post that contains sensitive data. I can't post full links, here's the end of the link: shell-programming-and-scripting/94965-help-shell-scripting-modify-user-creation-script-oracle-database.html
It's got a lot of data that should never be posted on... (2 Replies)
Discussion started by: JonHeller
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I have posted some data on the forum which needs to be deletd ASAP.
The post here in question are
How to do in this in shell script?
How to modify this script?
How to resolve this error?
Error in code in linux?
Please remove all the parts from post :
i-d4411185 ... (6 Replies)
All,
I'm hoping someone can help fill me in on this one.
:confused:
I work with bank data deemed "sensitive" and, once processed, need to figure out a way to overwrite the files with enough garbage data in order to prevent someone from being able to recover any of the data from the disk. I... (5 Replies)
Hello people,
In shell scripts if some sensitive data is set into the env so that it is available to other scripts called within those scripts -- Are there are security implications ?
-- I believe the scope of those environment variables ends with the execution of the script.
-- I see that... (4 Replies)
GETDATA(1) User Contributed Perl Documentation GETDATA(1)NAME
getData - retrieves databases from the Internet
SYNOPSIS
getData [ --mirrordir <path> ] <list of db names>
getData --list
DESCRIPTION
Bioinformatics has the intrinsic problem to bring the biological data to the end user. Astronomers have the equivalent problem and particle
physicists, well, they haven come up with (first) the web and (second) the computational grids to address their problems. Debian helps with
the programs but will not provide such huge datasets that are even frequently updated - not even in volatile.debian.org. Most
bioinformatics researchers will not need too many of such databases. And even more so will gladly continue in using public services
remotely.
For those who need a set of databases on a regular basis, this script shall be a start to automate the burden to download the data and
update indices and the like. The world has seen such magic before with the Lion Biosciences Prisma tool
(http://bib.oxfordjournals.org/cgi/reprint/3/4/389.pdf) but how about something simpler (as a start) that at least gets close to what we
desire and is Free. The aim must be to address the needs of all (most) communities, not only of the bioinformatics world. The seed was
hence made with databases from astronomy.
Please contact the Debian-Med community if you consider this program to be almost ready for your needs and explain what still needs to be
added. Public databases that you managed to integrate with this system are also very warmly welcomed as feedback.
OPTIONS --help
this help
--man
Present a more detailed description in form of a man page.
--verbose
Say one or two words more than required.
--mirrordir <path>
Specifies destination directory. The data will be mirrored to the folder $mirrordir/$dbname/. Please be aware that this mirrordir is
nowhere stored. The directory can consequently be moved to arbitrary locations at any time, if the users of the data are only informed
about that moving.
--list
Lists all databases that may be requested to be installed.
<list of db names>
Only those databases that are explicitly requested to be downloaded will be downloaded. Such databases may require considerable
bandwidth, so please make sure you know you are doing the right thing.
--post
Perform only the unpacking/indexing, but do not retrieve/update the databases. This option is considered useful when adding a new
database management system to the system, e.g. after installing EMBOSS.
--source
Perform only the unpacking/indexing, but do not retrieve/update the databases. This option may be beneficial when the site administator
is aware of current analyses that should not be disturbed by the indexing process but the downloading from the net can already be
started.
--confd <directory>
Allows for the specification of a directory in which multiple files can be stored that will be read by getData upon its invocation.
These may add values to the global variable %toBeMirrored that specifies the databases and their download scripts.
--config <system>
Preparation of the configuration file that would be reuired for a particular system that deals with the database. The configuration is
printed to stdout and is expected to be copied manually to the proper file or folder. One could imagine this process to be automated,
though this is not yet implemented. Currently available is support for two systems:
emboss This specifies the EMBOSS suite of tools for bioinformatics (www.emboss.org) that is also available as a Debian package. The
configuration for the Uniprot databases will allow the sequence retrieval with the seqret tool.
dre - ARC Grid Runtime Environment
Runtime environments (REs) are a concept of the ARC grid middleware of which more can be learned on http://www.nordugrid.org.
A script is needed to indicate the presence of a runtime environment. Here, the name of the script is important, which is not
definable by getData though since it only writes to stdout.
Unfortunately, the configuration was not yet be found to be modularised. It all needs to happen within the getData script itself.
--remove <list of dbnames>
This command removes folders that store the data. In principle this could be perfomed manually, though some databases may have special
requirements pre- or post-removal, which can be specified individually for every database.
SPECIFICATION OF DATABASES
Databases for download and their post-processing are specified at two different locations. One is the getData script itself, the other are
files stored in /etc/getData.d. Either will define elements of a considerably large hash. The key is the identifier which is also shown by
the 'getData --list' directive. The value is a reference to another hash, which assigns values to all the properties that a database has
for its download and post-processing:
name - a human-readable pretty-printed name or short description that makes clear to the world what this database is about.
A bad example is the mere assignment of "DE405", which few people understand. A better example is "Pfam-A : Manually curated protein
families and domains, only the seed is presented.". One could argue that one should have that field renamed to "description".
source - shell commands to perform the initial download and subsequent updates
Commonly the wget tool is used for download. The such presented little script is executed underneath the mirrordir directory. One
simple example is "wget --mirror ftp://ssd.jpl.nasa.gov/pub/eph/export/unix/unxp2[01]*.405". With increasing proficiency in using wget,
one is tempted to substitute "--mirror" with "--recursive --no-host-directories --no-directories --level 1 --no-parent".
post-download - shell commands to perform after the data has been downloaded.
A simple (and unnecessary when used the right flags to wget) example is the mere setting of a symbolic link:
"post-download" => "ln -s ssd.jpl.nasa.gov/pub/eph/export/unix/unxp*.405 ."
Some more effort has been put into TrEMBL for the merging of releases with subsequent updates and the indexing for EMBOSS:
"d=uncompressed; if [ ! -d $d ]; then mkdir $d; fi; "
."rm -rf $d/trembl.dat; "
."(find ftp.ebi.ac.uk -name '*.dat.gz' | xargs -r zcat ) > $d/trembl.dat; "
."[ -x /usr/bin/dbxflat ] "
. "&& cd $d && "
. "dbxflat -dbresource embl -dbname trembllocal -idformat swiss -filenames=trembl.dat -fields id,acc -auto",
The dots are connecting strings in Perl. This helps the readability of the code. When writing these scripts, please be aware the
newlines don't separate the individual commands here. Semicolon are required.
recommends - suggests a series of packages to be present for the use of the database or the performance of the indexing.
This information is not used at the moment, also to render this script more useful for other Linux distributions than Debian.
getWgetOptions - private command to get wget options
This is used at download time by makefiles, is not intended to be used interactively, and could be removed anytime.
EXAMPLES
The following will list the identifiers and the descriptions of the first 4 databases that area available via getData on your system.
./getData --mirrordir=/local/databases/mirrored --list | head 4
To install any particular database, only give its name as an argument. If the installation is performed at another directory than the
default, then the --mirrordir needs again to be set.
./getData swiss.dat
To remove the database again, give the script a hint with the --remove flag
./getData --remove swiss.dat
To perform the indexing only and circumvent the download (attention, this is dangerous since the index files will look newer than the
database is), do
./getData --post swiss.dat
A special exception to these extra scripts is the --config flag in that it takes a list of extra arguments. Each shall denote a particular
system that this database may be of interest for. There are today two systems supported:
TODO
We now need a mechanism with which packages can specify hooks that shall be called upon an update of a database. But we cannot assume that
every indexing that can be performed because of the installation of some package is also desired by the user. How to configure this
properly is left to be decided.
SEE ALSO
http://debian-med.alioth.debian.org, http://wiki.debian.org/DebianMed, /etc/getData.conf
AUTHORS
This script was prepared by Steffen Moeller <moeller@debian.org> and Charles Plessy <debian-no-spam@plessy.org> and is distributed under
the terms of the GNU Public License (GPL). On Debian systems, this license can be found under /usr/share/common-licenses/GPL.
perl v5.12.4 2011-08-03 GETDATA(1)