basedb-users — General BASE mailing list

RE: [base] local-infile option

[joe d. <jo...@uc...>]

Hi,
it looks like Audrey and I have exactly the same problem.  I can load loc=
al
data
infile fine when I am logged into mysql as root or Base, but Base itself
cannot do this.

Just to clarify then, Jim you are suggesting the compile mysql from sourc=
e
(the tarball...?) with the --enable-local-infile during the install.  So =
the
RPM has it turned off in some irreversible way, but only for PHP clients?

I have to admit, I am pretty new to linux and mysql, but why does Base ne=
ed
to do load data local infile instead of just doing load data infile, and
giving the baseuser file priviledge in mysql? The file being loaded is in=
 a
tmp directory on the server anyway, right?

I guess bottom line I will do what ever is the fastest thing to get this =
up
 and running. Do I need to uninstall the old RPM of mysql first, or while
the new
server just write over it?

Thanks for any advice you all can give me,
joe

-----Original Message-----
From: bas...@li...
[mailto:bas...@li...]On Behalf Of James
MacDonald
Sent: Wednesday, November 13, 2002 6:15 AM
To: bas...@li...
Subject: Re: [base] local-infile option


I couldn't ever get the local-infile option to work either. I ended up
having to compile from source (which is much more fun anyway ;-D). If you
take this option, remember to add --enable-local-infile to your configure
statement.

Jim



James W. MacDonald
UMCCC Microarray Core Facility
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> abi...@na... 11/12/02 12:41PM >>>
Hello,

I used RPM to install Mysql (v 3.23.53a) and apparently, the local-infile
option is disable. so I can't  use LOAD DATA LOCAL.
I try to add the line "local-infile=3D1" in the my.cnf file as indicated =
in
the
BASE README file, but it doesn't work.

How can I get through it ?
Thanks.


*-----------------------*
 Audrey Bihouee
 INSERM U533
 Facult=E9 de m=E9decine,
 1, rue Gaston Veil
 44035 Nantes Cedex 1
 Tel : 02.40.41.29.86
*-----------------------*



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Re: [base] Re: Hmm problem with BASE patch??

[Darrin T. <d.t...@im...>]

DOH!!
How silly do I feel :-(  You were right Carl, a corrupted file.  After I 
downloaded the patch again from the Telia sit this time it worked fine :-)
Thanx
Darrin

Carl Troein wrote:

>Darrin Taylor writes:
>
>>Hi Everyone,
>>I just tried the base1.0.6->base1.0.7a patch file.  It went fine until:
>>Patching file base_data.sql using Plan A...
>>Hunk #1 succeeded at 3.
>>Hmm...patch: **** malformed patch at line 333: Only in 
>>base-1.0.6/contrib: format_conversion
>>
>>then stopped
>>My base still seems fine, so any ideas??
>>
>
>Hmm... I don't have a whole lot of experience with patch, and it's not
>something I've seen before. Could it be that your version of patch is
>incompatible with my diff, or is maybe the file corrupted?
>Was the stuff in www patched (e.g. does BASE report itself as 1.0.7?)
>
>//Carl
>

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Microarray Computational Manager
Institute for Molecular Bioscience
University of Queensland 4072 AUSTRALIA
Email:     d.t...@im...
phone:     61-7-3365-4045
fax :    61-7-3365-4388
http://microarray.imb.uq.edu.au/

[base] Re: Hmm problem with BASE patch??

[Carl T. <ca...@th...>]

Darrin Taylor writes:

> Hi Everyone,
> I just tried the base1.0.6->base1.0.7a patch file.  It went fine until:
> Patching file base_data.sql using Plan A...
> Hunk #1 succeeded at 3.
> Hmm...patch: **** malformed patch at line 333: Only in 
> base-1.0.6/contrib: format_conversion
> 
> then stopped
> My base still seems fine, so any ideas??

Hmm... I don't have a whole lot of experience with patch, and it's not
something I've seen before. Could it be that your version of patch is
incompatible with my diff, or is maybe the file corrupted?
Was the stuff in www patched (e.g. does BASE report itself as 1.0.7?)

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Re: Compiling BASE

[Carl T. <ca...@th...>]

Leo Genyuk writes:

> I was trying to compile C++ portion of base 1.07 and ran into the 
> follwoing error:
> 
> # pwd
> /web-docs/base/exec/source
> # make depend
> make: Fatal error in reader: Makefile, line 17: Macro assignment on 
> dependency line

Which version of make are you using? I'm fairly sure any reasonably
new version of GNU make should work, but other implementations of
make (such as Sun's) probably miss some of the required functionality.

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Compiling BASE

[Leo G. <le...@ma...>]

I was trying to compile C++ portion of base 1.07 and ran into the 
follwoing error:

# pwd
/web-docs/base/exec/source
# make depend
make: Fatal error in reader: Makefile, line 17: Macro assignment on 
dependency line
#

This is line 17, 18 and 19:
all: WHAT = all
all: $(FILES) $(MAKEFILES)
       @echo -e "\nAll done\nDon't forget to \e[1mmake install\e[0m."

Did anyone else have this issue?

Thanks,

Leo.

RE: [base] Compile source code clustering

[Cao, X. (Sherry) <Xia...@ge...>]

Hi Julien:

GD is an ANSI C library for the dynamic creation of images. I downloaded the
source file from the following website.  http://www.boutell.com/gd/  Hope
this is useful for you.

Sherry Cao

-----Original Message-----
From: fa...@po... [mailto:fa...@po...] 
Sent: Tuesday, November 12, 2002 6:57 AM
To: ba...@th...
Subject: [base] Compile source code clustering

Hello everybody,

I'm writing because I have a problem to compile source code in exec/source 
directory

i want to compile code in clustering's directory...but i need gd.h and i
don't 
where is this file ?? 

Could you help ? How do you compile this code ?

I'm on Mandrake 8.1

Thanks in advance and I apologyse for my english

Julien Faurie

[base] Re: BASE performance/limits

[Carl T. <ca...@th...>]

kh...@sf... writes:

> I am interested to find out what the limits of BASE are. 

Me too.

> I suppose that the amount of experiments that one can store and analyze 
> depends mostly on the underlying relational database, operating system 
> and computer hardware. But there might be some performance issues related 
> to the design of BASE itself as well, right? (Please correct me if I'm 
> wrong!)

There certainly could, and there are a few places that could really be
bottlenecks, such as the RawBioAssayData and GeneListGene tables.

> Specifically: Has anybody used BASE for dealing with data from more than 
> 10,000 hybridizations, accessed by 20-30 researchers (not necessarily 
> simultaneously)? 

300-some hybridizations and 10 million rows in RawBioAssayData here,
and no complaints from the users yet.

> Any estimates on what hardware setup would be required for that type of 
> scenario (CPU, RAM, disk-space, etc.)?

Two CPUs per concurrent user is at least an upper limit for what's
useful, I'd say. Disks fast as hell, and lots of RAM, but I really
don't know how much, what CPUs, etc. would be needed for reasonable
performance.

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Hmm problem with BASE patch??

[Darrin T. <d.t...@im...>]

Hi Everyone,
I just tried the base1.0.6->base1.0.7a patch file.  It went fine until:
Patching file base_data.sql using Plan A...
Hunk #1 succeeded at 3.
Hmm...patch: **** malformed patch at line 333: Only in 
base-1.0.6/contrib: format_conversion

then stopped
My base still seems fine, so any ideas??
BTW great job guys :-)
Cheers
Darrin

-- 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Microarray Computational Manager
Institute for Molecular Bioscience
University of Queensland 4072 AUSTRALIA
Email: 	d.t...@im...
phone: 	61-7-3365-4045
fax :	61-7-3365-4388
http://microarray.imb.uq.edu.au/

[base] result file format

[Huang, F. <FX...@tx...>]

Dear all:

I always have problem when I map my clone ID as the ReportID in BASE
database during the 
result file format setting. 

The error message is: 
Error: Bad column number for field #4, 'ReporterID': 7 isn't between 1 and 0
(the number 
of columns you've entered for this format)

But actually my clone ID is something like 2516661. I am lost, any tips
appreciated.

Thanks a lot.

fang huang

[base] Re: Unable to load ResultFile

[Carl T. <ca...@th...>]

Audrey bihouee writes:


> The used command is not allowed with this MySQL version
> 
> I thought, that was because the option local-infile was disable, but when I try 
> LOAD DATA LOCAL INFILE directly in mysql, it works.

The local infile option can be enabled _per client_, so it's possible
that your 'mysql' tool has it on whereas for PHP it's off. Is there by
any chance a line with "local-infile=1" in the [mysql] section of your
my.cnf? (I'm not sure how the MySQL client library handles that file,
but the section names correspond to the names of executables or
possibly processes.)

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Unable to load ResultFile

[Audrey b. <abi...@na...>]

Hello,
I try to add a raw result file to my hybridization, I have this error : 
Parsing raw result file and adding data - please have patience.
Processed lines: [125] [846] [1564] [2281] 
Unable to load data into database

When I look into the httpd error.log, I find this error : 

MySQL query failed: "LOAD DATA LOCAL INFILE 
'/var/local/base/data/tmp/10360_0b3c5b41' REPLACE INTO TABLE 
RawBioAssayData (rawBioAssay, element, molecule, block, numCol, numRow, 
x, y, dia, FCh1Median, FCh1Mean, FCh1SD, BCh1Median, BCh1Mean, 
BCh1SD, percCh1SD1, percCh1SD2, percCh1Sat, FCh2Median, FCh2Mean, 
FCh2SD, BCh2Median, BCh2Mean, BCh2SD, percCh2SD1, percCh2SD2, 
percCh2Sat, ratiosSD, rgnRatio, rgnR2, FPixels, BPixels, flags, MValue, CV=
)" : 
The used command is not allowed with this MySQL version

I thought, that was because the option local-infile was disable, but when =
I try 
LOAD DATA LOCAL INFILE directly in mysql, it works.

Does anybody can help me ?
Thanks.

*-----------------------*
 Audrey Bihouee
 INSERM U533
 Facult=E9 de m=E9decine,
 1, rue Gaston Veil
 44035 Nantes Cedex 1
 Tel : 02.40.41.29.86
*-----------------------*

[base] Re: data analysis

[Carl T. <ca...@th...>]

Cao, Xiaohong (Sherry) writes:

> The problem I have now is that the job doesn't seem to run properly.  I got 
> this message in the "Plug-in output" section: 
> nice: argument must be numeric.
> nice: usage: nice [-n increment] utility [argument ...]
> *** Program returned 2

How odd. The only thing I can think of is that maybe your version
of nice (what version is it?) doesn't like something like
"nice -n5 program"
and instead wants
"nice -n 5 program".
Could you verify this? If that's the case, it should be easy enough
to do the required changes, and GNU nice doesn't care if there's a
space there or not.

> Also, when I ran jobController.php <jobid> locally, I got this error 
> message:
> Mysterious GET variable '_/jobController_php+10' in 

Mysterious it is. For some reason the entire command line ends up
in QUERY_STRING, and it definitely should not. I've never seen
anything like it. What version of PHP is this?

> Job status error for job 10 (not 'init' or 'error')

This is the error you get if you try to run jobController on
a job that is in neither of those two states. Usually, you wouldn't
want to run the same job again after success, nor would you start
a job again if it's already running. But there is a keyword
"force" that you can give on the command line after the jobid
if you want to re-run a job.

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Re: reporter filtering

[Carl T. <ca...@th...>]

Cao, Xiaohong (Sherry) writes:

> I just noticed that the wild card % does not work for "_" when I wanted to
> filter a reporter list.  Has anybody else had this problem?

Filter a reporter list? Do you mean that you're on the 'Reporters'
page and you want to filter on something to make a reporter list,
or something else?
If it's filtering on the reporter ID we're talking about, there
are some problems with using wildcards. In version 1.0.7 it's
possible to use wildcards with reporter ids, although it's probably
be slower than it should be.

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Re: Unable to load data into database

[Carl T. <ca...@th...>]

joe writes:

> I am having trouble loading raw data sets into the database.  Base seems to 
> successfully parse the file, but then cannot seem to load it.  This may be 
> the same problem as the local-infile option file, but Base does not seem to 
> have trouble loading other information into mysql tables.   Therefore I do 
> not think it is a problem with permissions, or evidently with disk space.  Is 
> there something fundamentally different in the way that BASE loads parsed raw 
> data rather than anything else into the mysql tables?  Could my problem be 
> the local-infile option (I too used the RPM).  

LOAD DATA LOCAL INFILE is used in just a few places, where a large
number of rows are inserted at the same time: result files, plates,
gene lists, when jobs finish, and possibly a few others.
If you're using an RPM binary version of MySQL, and you haven't
done anything to get LOCAL INFILE to work, I'd guess that that's
causing the trouble, but I can't be sure without seeing the errors
that you get (most importantly any logged SQL errors).
If LOCAL INFILE is the problem, make sure mysqld is started with
--local-infile=1. (and test that it works, too)

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Re: Intensity values

[Carl T. <ca...@th...>]

Sanchita Bhattacharya writes:

> Hi,

Hey, dude, your date and time are way off. Windows doesn't ship
with ntpd (hardly surprising for an OS that doesn't even ship with
a compiler), but you can doenload e.g. NetTime and use it to keep
your computer's clock from running off into the future.

> I have noticed that when the intensity values are loaded in to BASE they are
> truncated to round figures loosing the real value. Data type for these
> fields needs to be changed as I think one would like to see the same value
> as it appears in the raw data file
> 
> Hope everybody agrees to it.

Yep, that's a change that's already been done in the CVS after a
discussion a while back. Or actually, the CVS version will let you
pick whichever data type you wish, but the default setup is the
1.0.x one with FLOAT instead of SMALLINT.

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] BASE 1.0.7a

[Carl T. <ca...@th...>]

With the mailing list being down and all, I almost forgot to
say that I've released BASE 1.0.7, which includes fixes to a
few bugs that have been discussed on the mailing list, as well
as a beta version of a new plot tool (in Java) that Mats Attnäs
has been working on. Shortly after I released 1.0.7 I replaced
it with 1.0.7a, since the mailing list subscription address was
wrong and I forgot to update the version number. (I just keep
doing that. :-P)

//Carl

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se

[base] Re: (no subject)

[Carl T. <ca...@th...>]

James MacDonald writes:

> Maybe that is part of their privacy policy...

LOL! :-D

//Carl - thinking about adding an outrageous disclaimer to his .sig

-- 
 Carl Troein - ca...@th...
 http://www.thep.lu.se/~carl/
 BASE developer - http://base.thep.lu.se
 DISCLAIMER: This message was not indended for you and you have no
  right to read it, reply to it, or even delete it from your inbox,
  let alone download it from the mail server. If you fail to comply
  with these terms, I will persecute you to the full extent of the
  DMCA and any other phoney law I can find.
  

[base] array template/map changes

[Matthew S. <ms...@ph...>]

So this is a combination question/feature request.  The issue works out
something like this:

we have several array templates (or maps, call them what you will) with the
names and locations of all the genes run on our arrays.  Since no-one here
(or anywhere else, I would imagine) wants to re-parse the data and create a
new .gpr file (raw data file), it would be a whole lot easier to just have
an additional tab to group raw data sets into array maps, and then simply
change the array map, and have the changes apply to all raw data which are
included in the map group...

Since I'm fairly sure that this functionality doesn't exist in base, the
question is, is anyone working on doing it?  If not, I would think that
actually incorporating a change like that would require some changes on the
main pages as well as writing the array-map functions out.

Thanks,



---
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[base] BASE performance/limits

[<kh...@sf...>]

Hi BASE users,

I am interested to find out what the limits of BASE are. 
I suppose that the amount of experiments that one can store and analyze 
depends mostly on the underlying relational database, operating system 
and computer hardware. But there might be some performance issues related 
to the design of BASE itself as well, right? (Please correct me if I'm 
wrong!)
Specifically: Has anybody used BASE for dealing with data from more than 
10,000 hybridizations, accessed by 20-30 researchers (not necessarily 
simultaneously)? 
Any estimates on what hardware setup would be required for that type of 
scenario (CPU, RAM, disk-space, etc.)?

Just from following the discussions and from glancing shortly over a local 
installation I am pretty excited about BASE. 
Hopefully it will be suitable for our needs!

Thanks for any information you can provide,

	Karsten
-- 
Karsten Hokamp, PhD          Phone: (001)-604-291-4206
MBB, Brinkman Lab            Email: kh...@sf...
Simon Fraser University      WWW  : www.sfu.ca/~khokamp
Burnaby, Greater Vancouver, British Columbia, Canada

[base] plug-in for GeneSight

[Cao, X. (Sherry) <Xia...@ge...>]

Hi,

I am wondering if there is a plug-in or similar sort so people can export
data to GeneSight for data analysis?

Sherry

RE: [base] Re: data analysis

[Cao, X. (Sherry) <Xia...@ge...>]

Hi Carl:

The $config["execDir"] was set correctly in the config.inc.php.
I thought probably it was because of php was not set to run as CGI 
executable so I recompiled it and it seem to be able to start the job fine.

The problem I have now is that the job doesn't seem to run properly.  I got 
this message in the "Plug-in output" section: 
nice: argument must be numeric.
nice: usage: nice [-n increment] utility [argument ...]
*** Program returned 2
Also, when I ran jobController.php <jobid> locally, I got this error 
message:
Mysterious GET variable '_/jobController_php+10' in 
Job status error for job 10 (not 'init' or 'error')

Thanks for all the help as always.

Sherry

-----Original Message-----
From: Carl Troein [mailto:ca...@th...] 
Sent: Wednesday, November 13, 2002 8:46 AM
To: ba...@th...
Subject: [base] Re: data analysis


Cao, Xiaohong (Sherry) writes:

> I have a similar question to Zhilin about data analysis.  I was able to
> start the job to normalize the dataset using LOWESS but the job was not
> finished.  I have never got a result file but I did get an error message
in
> the apache error_log  saying 
> 
> sh:  ~/base/exec/jobController.php: not found
> 
> the "exec" directory is in the PATH so I am not quite sure what went
wrong.
> Also, there is no job id listed in the data/jobs directory.

It sounds like $config["execDir"] is not correct. Make sure
that it really points to the 'exec' directory, and note that
you should NOT use ~ to denote the path to your home directory -
tilde expansion is something the shell does, not a feature of
the file system itself, so although tilde expansion might work
sometimes (e.g. when PHP's exec() function is used), it's not
reliable.

//Carl

[base] reporter filtering

[Cao, X. (Sherry) <Xia...@ge...>]

Hi,

I just noticed that the wild card % does not work for "_" when I wanted to
filter a reporter list.  Has anybody else had this problem?

Sherry 

[base] Unable to load data into database

[joe <jo...@uc...>]

HI,
I am having trouble loading raw data sets into the database.  Base seems =
to=20
successfully parse the file, but then cannot seem to load it.  This may b=
e=20
the same problem as the local-infile option file, but Base does not seem =
to=20
have trouble loading other information into mysql tables.   Therefore I d=
o=20
not think it is a problem with permissions, or evidently with disk space.=
  Is=20
there something fundamentally different in the way that BASE loads parsed=
 raw=20
data rather than anything else into the mysql tables?  Could my problem b=
e=20
the local-infile option (I too used the RPM). =20
Any suggestions of things to try would be appreciated.
joe

[base] Bioassay Sets

[Sanchita B. <san...@MI...>]

Hi,

I would like to view two Bioassay sets of a experiment in one window in
EExplorer but couldn't do it. Two Bioassays can be viewed but not two
Bioassay sets. Has anybody tried to look into this matter.


Thanks,
Sanchita

[base] Intensity values

[Sanchita B. <san...@MI...>]

Hi,

I have noticed that when the intensity values are loaded in to BASE they are
truncated to round figures loosing the real value. Data type for these
fields needs to be changed as I think one would like to see the same value
as it appears in the raw data file

Hope everybody agrees to it.



Sanchita