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From: <ja...@op...> - 2001-03-07 18:15:16
|
Hey, So the good news is, you should have a completely working installation, but for some reason dtd2html is crapping-out. All this means is that you might not be able to view the the html-ized dtd files. The rest should all work properly. > dtd2html > Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line > 1475, within pattern > (Missing operator before ?) > Scalar found where operator expected at /usr/local/lib/perl/dtd.pl line > 1475, within pattern > (Missing operator before ?) > syntax error at /usr/local/lib/perl/dtd.pl line 1475, near "$opt$plus" It seems you have a different version of dtd.pl ... In my version there is nothing at line 1475, and the only occurrence of "$opt$plus" is in extract_elem_names() at line 1522. Did you install the version from the tarball on sourceforge, i.e. perlSGML.2001Jan23.tar.gz? If so what version of perl are you using (silly me for not storing that info in Options.reminders... > > Did the dir: '/usr/local/genex/lib/dtd/' get made OK and is set to be writable? > > It seems that it made ok & it's writable only to root though. Do I need to > change it be group writeable? > > hammerhead@hammerhead:/$ ls -ld /usr/local/genex/lib/dtd > drwxr-sr-x 3 root staff 4096 Feb 26 17:30 > /usr/local/genex/lib/dtd > hammerhead@hammerhead:/$ ls -l /usr/local/genex/lib/dtd > total 56 > -rw-r--r-- 1 root staff 1772 Feb 26 17:30 als.dtd > -rw-r--r-- 1 root staff 2024 Feb 26 17:30 ams.dtd > -rw-r--r-- 1 root staff 1633 Feb 26 17:30 csf.dtd > lrwxrwxrwx 1 root staff 24 Feb 26 17:30 dtd -> > /usr/local/genex/lib/dtd > drwxr-sr-x 2 root staff 4096 Feb 26 16:21 genexml-html > -rw-r--r-- 1 root staff 34788 Feb 26 17:30 genexml.dtd > -rw-r--r-- 1 root staff 3199 Feb 26 17:30 usf.dtd check inside the genexml-html directory for a lot of html files. If they exist, then perhaps it really did work after all. jas. |
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From: Harry M. <hj...@ta...> - 2004-04-19 21:55:24
|
Yup, this is a result of setting the GENEX_HOST to something other than localhost. Hooray! we picked up a real bug! OK - I'm looking at this right now. For now tho, change GENEX_HOST back to 'localhost' and try again. hjm hde...@gm... wrote: > Harry, > > Here is the concerned segment of the config file: > > the email of the local person to bug with problems with GeneX > 'CONTACT_EMAIL' => 'hde...@gm...', > > # > # set this to 'localhost' if you want the DB to be local-only > # set it to the actual hostname if the DB is to be remote-accessible > 'GENEX_HOST' => 'wellerlab1.binf.gmu.edu', > > # > # this is the Fully Qualified Domain Name of the install machine > 'WWW_HOST' => 'wellerlab1.binf.gmu.edu', > > # > # this indicates where the files for genex are rooted > 'LOCAL_DIR' => '/usr/local', > > # > # this is the root name of the genex installation on the file system > # and from the web server (-> /usr/local/genex) > 'GENEX_DIR' => 'genex', > > Thx, > Hrishi > > > ____________________________________________________________________ > > 'Life's battles don't always go to the stronger or faster man. But sooner or later the man who wins is the one who thinks he can.' > -Walter D. Wintle > > > ----- Original Message ----- > From: Harry Mangalam <hj...@ta...> > Date: Monday, April 19, 2004 5:25 pm > Subject: [Genex-users] Re: > > >>This error is due to an unsubstituted variable (%%GENEX_PORT%%) >>making it thru >>the substitution script. This should never happen. It's supposed >>to be >>substituted to 5432 and replaced everywhere it occurs. >> >>Hrishi - did you set up the DB to be TCP-available or just >>localhost? ie what is >>the GENX_HOST line in your GeneX.config file? >> >>teh localhost version would look like this: >> >>'GENEX_HOST' => 'localhost', >> >> >>Jason - have you seen this before? Is this a problem with making >>the pg DB >>TCP-available instead of just localhost? I have to admit that I >>don't remember >>making it TCP-available recently, but I'll check it out. >> >>hjm >> >> >>hde...@gm... wrote: >> >>>Hi Harry, >>> >>>For the pg_nba.conf,was just a bit puzzled with IPs,one IP is >> >>for local host and the second is the the IP of the machine on >>which genex is being installed?! >> >>>But i think i figured it out. >>>I edited the GeneX.config file and was at make install step,i >> >>have already sent email about this,just incase you did not receive >>it (my skl's email is slow), here is the error which i encountered: >> >>>Ok, this will take a few minutes, hit [Enter] to proceed. >>> >>>Perl/scripts/gendb.pl --db genex --dir /home/deshmuk/genex- >> >>server --user genex --pass xxxx --no_ecoli_sf >> >>>Creating DB ... >>> /usr/local/genex/bin/create-genex-db.pl --dbname genex -- >> >>username genex --password hyde00 --rootdir /home/deshmuk/genex- >>server /home/deshmuk/genex-server/DB/xml/GENEX_ARRAY.xml >>/home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_DESIGN.xml >>/home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_MANUFACTURE.xml >>/home/deshmuk/genex-server/DB/xml/GENEX_AUDIT.xml >>/home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL.xml >>/home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_CHARACTERISTIC.xml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHANGELOG.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHROMOSOME.xml /home/deshmuk/genex-server/DB/xml/GENEX_CITATION.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTACT.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTROLLED_VOCAB.xml /home/deshmuk/genex-server/DB/xml/GENEX_ >>DATABASE.x......................... >> >>>DBI >> >>connect('dbname=template1;host=wellerlab1.binf.gmu.edu;port=%%GENEX_PORT%%','genex',...) failed: could not connect to server: Connection refused at /usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm line 196 >> >>>Couldn't connect to template1: could not connect to server: >> >>Connection refused at >>/usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm line 201. >> >>>Died at Perl/scripts/gendb.pl line 108. >>> >>> FATAL ERROR >>> >>>I got an error when I ran the DB installer. >>> >>> >>>!! System Error: @ line: 341 (su -c '/usr/bin/perl >> >>/home/deshmuk/genex-server/Perl/scripts/db.pl' postgres) >> >>> FATAL ERROR >>> >>>I got an error when I ran the DB installer. >>> >>>make: *** [install] Error 9 >>> >>> >>>Waiting for your reply. >>> >>>Thanks, >>>Hrishi >>> >>> >>> >>> >>> >>> >>>>Hi Hrishi, >>>> >>>>Good point of clarification. >>>> >>>>If you install postgres as per the apt-get line you mention in >> >>1), >> >>>>you should >>>>not have to do much else, besides following the instructions in >>>>the section marked: >>>> >>>> >>>>Modify configuration files: >>>>=========================== >>>>1- ... >>>> >>>>2 - modify the Postgresql config file for GeneX: >>>> >>>>which tells you how to modify the PG config file. >>>> >>>>The lines: >>>> >>>> >>>>> For the basic postgres installation, please see: >>>>> http://www.postgresql.org/docs/7.4/interactive/installation.html >>>> >>>>point you to the documentation that tell you how to do the basic >>>>postgres >>>>installation. (You should understand the basics of how the >> >>system >> >>>>works.)However the specifics are mentioned in the postgres stanza >>>> >>>>hde...@gm... wrote: >>>> >>>> >>>>>Hi Harry, >>>>> >>>>>Couple of "silly" questions: >>>>> >>>>>I have been following the instructions/guidelines given in the >>>> >>>>INSTALL documnet in the latest genex-server dir (did svn >>>>.............)> >>>> >>>> >>>>>1) I did: >>>>>The following commands pasted into a root shell will install >>>> >>>>most of >>>> >>>> >>>>>the pre-requisites you need to support GeneX : >>>>> >>>>>apt-get update >>>>> >>>>>apt-get install postgresql postgresql-dev postgresql-client >>>> >>>>postgresql-doc \ >>>> >>>> >>>>>libpgtcl libpgperl pgaccess unixodbc-bin expat perlSGML apache- >>>> >>>>dev \ >>>> >>>> >>>>>libapache-mod-perl libdevel-symdump-perl odbc-postgresql >>>> >>>>libpgjava \ >>>> >>>> >>>>>perl-modules libterm-readkey-perl libapache-session-perl \ >>>>>libapache-request-perl libdbd-pg-perl libdbi-perl \ >>>>>libhtml-mason-perl libtie-ixhash-perl libxml-xerces-perl r- >> >>base- >> >>>>core \ >>>> >>>> >>>>>r-recommended r-base r-base-dev r-base-html odbc-postgresql >>>> >>>>libiodbc2 \ >>>> >>>> >>>>>unixodbc libpgjava pgaccess unixodbc-bin postgresql-client >>>> >>>>postgresql-doc \ >>>> >>>> >>>>>libecpg-dev libpgtcl libdbd-pgsql >>>>> >>>>>Now the question is do i have to install postgresql , as per >> >>the >> >>>>instructions given @ >>>> >>>> >>>>>2 - modify the Postgresql config file for GeneX: >>>>> >>>>> For the basic postgres installation, please see: >>>>> http://www.postgresql.org/docs/7.4/interactive/installation.html >>>>> >>>>>OR does it mean that when i did step (1) postgresql was >>>> >>>>installed and i can skip the link and what it says??!! >>>> >>>> >>>>>Now at the step of enabling GeneX2 DB for remote access via >> >>TCP, >> >>>>one IP is the local host, the second IP should be the IP of the >>>>machineon which genex is being installed?! >>>> >>>>The paragraph below that tells what the 2 numbers are: >>>> >>>> >>>># TYPE DATABASE USER IP-ADDRESS IP-MASK >> >> >> >>>>METHOD >>>>host all all 127.0.0.1 >> >>255.255.255.255 >> >>>>password >>>>host genex all 192.168.1.0 255.255.255.0 >> >> >> >>>>password >>>> >>>> In the above example, the first line allows all users from >> >>the >> >>>>local machine >>>> to access all databases as long as they provide valid >>>>passwords. The second >>>> line allows machines from a private subnet (192.168.1.0, masked >>>> 255.255.255.0) to access only the genex DB and only if they >>>>are known >>>> postgres users and supply the correct postgresql password. >>>>There are more >>>> (and less) stringent authentication schemes described in the >>>>comments in >>>> 'pg_hba.conf'. >>>> The two net address fields specify to which client machines a >>>>host or >>>> hostssl record applies, based on their IP address. The >>>>precise logic >>>> is that the (actual-IP-address XOR IP-address-field) AND IP- >>>>mask-field must >>>> be zero for the record to match. >>>> >>>> >>>> >>>>>Trivial/silly, i thought it was good to clarify just in case >> >>and >> >>>>may be add a >>>>line or two in the INSTALL doc that resolves these "silly" >> >>questions.>> >> >>>>what part of the above is unclear? Did you read the comments in >>>>the pg_hba.conf >>>>file? I admit, it's not drop-dead simple, but it's the way >>>>postgres works and >>>>if you don't understand the postgres basics, you won't be able >> >>to >> >>>>administer the >>>>system. >>>> >>>> >>>> >>>> >>>>>Waiting for your reply. >>>>> >>>>>Thanks, >>>>>Hrishi >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>>-- >>>>Cheers, Harry >>>>Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... >>>> <<plain text preferred>> >>>> >>> >>> >>-- >>Cheers, Harry >>Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... >> <<plain text preferred>> >> >> >>------------------------------------------------------- >>This SF.Net email is sponsored by: IBM Linux Tutorials >>Free Linux tutorial presented by Daniel Robbins, President and CEO of >>GenToo technologies. Learn everything from fundamentals to system >>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click >>_______________________________________________ >>Genex-users mailing list >>Gen...@li... >>https://lists.sourceforge.net/lists/listinfo/genex-users >> >> > > > -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... <<plain text preferred>> |
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From: Harry M. <hj...@ta...> - 2004-04-19 22:57:31
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Hi Hrishi,
please write to the dev list. otherwise no one else will be able to benefit
from your questions.
hde...@gm... wrote:
> Harry,
>
> I did modify the pg_hba.conf file,i put the configuration as suggested by the INSTALL
doc at the end of the file but i guess it has to be at the "Put you
configuration here" line.
I don't follow what the above bit means. YOu can put it anywhere, but if
there'a a later config line that contradicts or modifies its impact, it will
take teh later one.
> Do i need to install Bio-Perl!!!!
Apparently. Don't for get to do a make configure each time before you run make
install.
> Its just set for localhost and here is the new error i am getting:
> Finished
> Finished
> Adding mas5-short QuantitationTypeDimension ...
> /usr/local/genex/bin/qtdim-insert.pl --dbname genex --username genex --password hyde00 /home/deshmuk/genex-server/DB/curated_data/qtdim-mas5-short.xml --name=MAS-short --abbrev_name=dmas5s --version=5.0 --feat="0" --data_start_regex1=^\s+ --data_end_regex=^$
> Can't locate Bio/MAGE.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.3 /usr/local/share/perl/5.8.3 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at /usr/local/genex/bin/qtdim-insert.pl line 14.
> BEGIN failed--compilation aborted at /usr/local/genex/bin/qtdim-insert.pl line 14.
> Died at Perl/scripts/gendb.pl line 226.
>
> FATAL ERROR
>
> I got an error when I ran the DB installer.
>
>
> !! System Error: @ line: 341 (su -c '/usr/bin/perl /home/deshmuk/genex-server/Perl/scripts/db.pl' postgres)
>
> FATAL ERROR
>
> I got an error when I ran the DB installer.
>
> make: *** [install] Error 9
>
>
> Thx,
> Hrishi
>
>
>
>
>>did you modify the pg_hba.conf file? Looks like you didn't.
>>
>>hjm
>>
>>
>>hde...@gm... wrote:
>>
>>>Harry,
>>>
>>>Here is the error when i edit .config file for just localhost.
>>>
>>>Ok, this will take a few minutes, hit [Enter] to proceed.
>>>
>>>Perl/scripts/gendb.pl --db genex --dir /home/deshmuk/genex-
>>
>>server --user genex --pass --no_ecoli_sf
>>
>>>Creating DB ...
>>> /usr/local/genex/bin/create-genex-db.pl --dbname genex --
>>
>>username genex --password hyde00 --rootdir /home/deshmuk/genex-
>>server /home/deshmuk/genex-server/DB/xml/GENEX_ARRAY.xml
>>/home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_DESIGN.xml
>>/home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_MANUFACTURE.xml
>>/home/deshmuk/genex-server/DB/xml/GENEX_AUDIT.xml
>>/home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL.xml
>>/home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_CHARACTERISTIC.xml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHANGELOG.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHROMOSOME.xml /home/deshmuk/genex-server/DB/xml/GENEX_CITATION.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTACT.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTROLLED_VOCAB.xml /home/deshmuk/genex-server/DB/xml/GENEX_
>>DATABASE.x.........................
>>
>>>DBI connect('dbname=template1','genex',...) failed: FATAL:
>>
>>IDENT authentication failed for user "genex" at
>>/usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm line 196
>>
>>>Couldn't connect to template1: FATAL: IDENT authentication
>>
>>failed for user "genex" at
>>/usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm line 201.
>>
>>>Died at Perl/scripts/gendb.pl line 108.
>>>
>>> FATAL ERROR
>>>
>>>I got an error when I ran the DB installer.
>>>
>>>
>>>!! System Error: @ line: 341 (su -c '/usr/bin/perl
>>
>>/home/deshmuk/genex-server/Perl/scripts/db.pl' postgres)
>>
>>> FATAL ERROR
>>>
>>>I got an error when I ran the DB installer.
>>>
>>>make: *** [install] Error 9
>>>
>>>
>>>AND
>>>
>>>Here is the errors from install-errors.txt
>>>!! System Error: No such file or directory @ line: 266 (cp
>>
>>Mason/workspace/edit/species-edit.html
>>/var/www/genex/mason/workspace/edit)>
>>
>>>!! System Error: @ line: 341 (su -c '/usr/bin/perl
>>
>>/home/deshmuk/genex-server/Perl/scripts/db.pl' postgres)
>>
>>>
>>>
>>>Thx,
>>>Hrishi
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>>This error is due to an unsubstituted variable (%%GENEX_PORT%%)
>>>>making it thru
>>>>the substitution script. This should never happen. It's
>>
>>supposed
>>
>>>>to be
>>>>substituted to 5432 and replaced everywhere it occurs.
>>>>
>>>>Hrishi - did you set up the DB to be TCP-available or just
>>>>localhost? ie what is
>>>>the GENX_HOST line in your GeneX.config file?
>>>>
>>>>teh localhost version would look like this:
>>>>
>>>>'GENEX_HOST' => 'localhost',
>>>>
>>>>
>>>>Jason - have you seen this before? Is this a problem with
>>
>>making
>>
>>>>the pg DB
>>>>TCP-available instead of just localhost? I have to admit that I
>>>>don't remember
>>>>making it TCP-available recently, but I'll check it out.
>>>>
>>>>hjm
>>>>
>>>>
>>>>hde...@gm... wrote:
>>>>
>>>>
>>>>>Hi Harry,
>>>>>
>>>>>For the pg_nba.conf,was just a bit puzzled with IPs,one IP is
>>>>
>>>>for local host and the second is the the IP of the machine on
>>>>which genex is being installed?!
>>>>
>>>>
>>>>>But i think i figured it out.
>>>>>I edited the GeneX.config file and was at make install step,i
>>>>
>>>>have already sent email about this,just incase you did not
>>
>>receive
>>
>>>>it (my skl's email is slow), here is the error which i encountered:
>>>>
>>>>
>>>>>Ok, this will take a few minutes, hit [Enter] to proceed.
>>>>>
>>>>>Perl/scripts/gendb.pl --db genex --dir /home/deshmuk/genex-
>>>>
>>>>server --user genex --pass xxxx --no_ecoli_sf
>>>>
>>>>
>>>>>Creating DB ...
>>>>> /usr/local/genex/bin/create-genex-db.pl --dbname genex -
>>
>>-
>>
>>>>username genex --password hyde00 --rootdir /home/deshmuk/genex-
>>>>server /home/deshmuk/genex-server/DB/xml/GENEX_ARRAY.xml
>>>>/home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_DESIGN.xml
>>>>/home/deshmuk/genex-server/DB/xml/GENEX_ARRAY_MANUFACTURE.xml
>>>>/home/deshmuk/genex-server/DB/xml/GENEX_AUDIT.xml
>>>>/home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL.xml
>>>>/home/deshmuk/genex-
>>
>>server/DB/xml/GENEX_BIOMATERIAL_CHARACTERISTIC.xml /home/deshmuk/genex-server/DB/xml/GENEX_BIOMATERIAL_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHANGELOG.xml /home/deshmuk/genex-server/DB/xml/GENEX_CHROMOSOME.xml /home/deshmuk/genex-server/DB/xml/GENEX_CITATION.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE.xml /home/deshmuk/genex-server/DB/xml/GENEX_COMPOSITE_SEQUENCE_LINK.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTACT.xml /home/deshmuk/genex-server/DB/xml/GENEX_CONTROLLED_VOCAB.xml /home/deshmuk/genex-server/DB/xml/GENEX_
>>
>>>>DATABASE.x.........................
>>>>
>>>>
>>>>>DBI
>>>>
>>>>connect('dbname=template1;host=wellerlab1.binf.gmu.edu;port=%%GENEX_PORT%%','genex',...) failed: could not connect to server: Connection refused at /usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm line 196
>>>>
>>>>
>>>>>Couldn't connect to template1: could not connect to server:
>>>>
>>>>Connection refused at
>>>>/usr/local/share/perl/5.8.3/Class/ObjectTemplate/DB/Connect.pm
>>
>>line 201.
>>
>>>>>Died at Perl/scripts/gendb.pl line 108.
>>>>>
>>>>> FATAL ERROR
>>>>>
>>>>>I got an error when I ran the DB installer.
>>>>>
>>>>>
>>>>>!! System Error: @ line: 341 (su -c '/usr/bin/perl
>>>>
>>>>/home/deshmuk/genex-server/Perl/scripts/db.pl' postgres)
>>>>
>>>>
>>>>> FATAL ERROR
>>>>>
>>>>>I got an error when I ran the DB installer.
>>>>>
>>>>>make: *** [install] Error 9
>>>>>
>>>>>
>>>>>Waiting for your reply.
>>>>>
>>>>>Thanks,
>>>>>Hrishi
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>Hi Hrishi,
>>>>>>
>>>>>>Good point of clarification.
>>>>>>
>>>>>>If you install postgres as per the apt-get line you mention in
>>>>
>>>>1),
>>>>
>>>>
>>>>>>you should
>>>>>>not have to do much else, besides following the instructions
>>
>>in
>>
>>>>>>the section marked:
>>>>>>
>>>>>>
>>>>>>Modify configuration files:
>>>>>>===========================
>>>>>>1- ...
>>>>>>
>>>>>>2 - modify the Postgresql config file for GeneX:
>>>>>>
>>>>>>which tells you how to modify the PG config file.
>>>>>>
>>>>>>The lines:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> For the basic postgres installation, please see:
>>>>>>>
>>
>>http://www.postgresql.org/docs/7.4/interactive/installation.html>>>>
>>
>>>>>>point you to the documentation that tell you how to do the
>>
>>basic
>>
>>>>>>postgres
>>>>>>installation. (You should understand the basics of how the
>>>>
>>>>system
>>>>
>>>>
>>>>>>works.)However the specifics are mentioned in the postgres stanza
>>>>>>
>>>>>>hde...@gm... wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Hi Harry,
>>>>>>>
>>>>>>>Couple of "silly" questions:
>>>>>>>
>>>>>>>I have been following the instructions/guidelines given in
>>
>>the
>>
>>>>>>INSTALL documnet in the latest genex-server dir (did svn
>>>>>>.............)>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>1) I did:
>>>>>>>The following commands pasted into a root shell will install
>>>>>>
>>>>>>most of
>>>>>>
>>>>>>
>>>>>>
>>>>>>>the pre-requisites you need to support GeneX :
>>>>>>>
>>>>>>>apt-get update
>>>>>>>
>>>>>>>apt-get install postgresql postgresql-dev postgresql-client
>>>>>>
>>>>>>postgresql-doc \
>>>>>>
>>>>>>
>>>>>>
>>>>>>>libpgtcl libpgperl pgaccess unixodbc-bin expat perlSGML
>>
>>apache-
>>
>>>>>>dev \
>>>>>>
>>>>>>
>>>>>>
>>>>>>>libapache-mod-perl libdevel-symdump-perl odbc-postgresql
>>>>>>
>>>>>>libpgjava \
>>>>>>
>>>>>>
>>>>>>
>>>>>>>perl-modules libterm-readkey-perl libapache-session-perl \
>>>>>>>libapache-request-perl libdbd-pg-perl libdbi-perl \
>>>>>>>libhtml-mason-perl libtie-ixhash-perl libxml-xerces-perl r-
>>>>
>>>>base-
>>>>
>>>>
>>>>>>core \
>>>>>>
>>>>>>
>>>>>>
>>>>>>>r-recommended r-base r-base-dev r-base-html odbc-postgresql
>>>>>>
>>>>>>libiodbc2 \
>>>>>>
>>>>>>
>>>>>>
>>>>>>>unixodbc libpgjava pgaccess unixodbc-bin postgresql-client
>>>>>>
>>>>>>postgresql-doc \
>>>>>>
>>>>>>
>>>>>>
>>>>>>>libecpg-dev libpgtcl libdbd-pgsql
>>>>>>>
>>>>>>>Now the question is do i have to install postgresql , as per
>>>>
>>>>the
>>>>
>>>>
>>>>>>instructions given @
>>>>>>
>>>>>>
>>>>>>
>>>>>>>2 - modify the Postgresql config file for GeneX:
>>>>>>>
>>>>>>> For the basic postgres installation, please see:
>>>>>>>
>>
>>http://www.postgresql.org/docs/7.4/interactive/installation.html>>>>>
>>
>>>>>>>OR does it mean that when i did step (1) postgresql was
>>>>>>
>>>>>>installed and i can skip the link and what it says??!!
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Now at the step of enabling GeneX2 DB for remote access via
>>>>
>>>>TCP,
>>>>
>>>>
>>>>>>one IP is the local host, the second IP should be the IP of
>>
>>the
>>
>>>>>>machineon which genex is being installed?!
>>>>>>
>>>>>>The paragraph below that tells what the 2 numbers are:
>>>>>>
>>>>>>
>>>>>># TYPE DATABASE USER IP-ADDRESS IP-MASK
>>
>>
>>
>>>>
>>>>
>>>>>>METHOD
>>>>>>host all all 127.0.0.1
>>>>
>>>>255.255.255.255
>>>>
>>>>
>>>>>>password
>>>>>>host genex all 192.168.1.0
>>
>>255.255.255.0
>>
>>>>
>>>>
>>>>>>password
>>>>>>
>>>>>> In the above example, the first line allows all users from
>>>>
>>>>the
>>>>
>>>>
>>>>>>local machine
>>>>>> to access all databases as long as they provide valid
>>>>>>passwords. The second
>>>>>> line allows machines from a private subnet (192.168.1.0, masked
>>>>>> 255.255.255.0) to access only the genex DB and only if they
>>>>>>are known
>>>>>> postgres users and supply the correct postgresql password.
>>>>>>There are more
>>>>>> (and less) stringent authentication schemes described in
>>
>>the
>>
>>>>>>comments in
>>>>>> 'pg_hba.conf'.
>>>>>> The two net address fields specify to which client machines
>>
>>a
>>
>>>>>>host or
>>>>>> hostssl record applies, based on their IP address. The
>>>>>>precise logic
>>>>>> is that the (actual-IP-address XOR IP-address-field) AND IP-
>>>>>>mask-field must
>>>>>> be zero for the record to match.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Trivial/silly, i thought it was good to clarify just in case
>>>>
>>>>and
>>>>
>>>>
>>>>>>may be add a
>>>>>>line or two in the INSTALL doc that resolves these "silly"
>>>>
>>>>questions.>>
>>>>
>>>>>>what part of the above is unclear? Did you read the comments
>>
>>in
>>
>>>>>>the pg_hba.conf
>>>>>>file? I admit, it's not drop-dead simple, but it's the way
>>>>>>postgres works and
>>>>>>if you don't understand the postgres basics, you won't be able
>>>>
>>>>to
>>>>
>>>>
>>>>>>administer the
>>>>>>system.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>>Waiting for your reply.
>>>>>>>
>>>>>>>Thanks,
>>>>>>>Hrishi
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>--
>>>>>>Cheers, Harry
>>>>>>Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
>>>>>> <<plain text preferred>>
>>>>>>
>>>>>
>>>>--
>>>>Cheers, Harry
>>>>Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
>>>> <<plain text preferred>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>This SF.Net email is sponsored by: IBM Linux Tutorials
>>>>Free Linux tutorial presented by Daniel Robbins, President and
>>
>>CEO of
>>
>>>>GenToo technologies. Learn everything from fundamentals to system
>>>>administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
>>>>_______________________________________________
>>>>Genex-users mailing list
>>>>Gen...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/genex-users
>>>>
>>>>
>>>
>>>
>>>
>>>
>>--
>>Cheers, Harry
>>Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
>> <<plain text preferred>>
>>
>
>
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
|
|
From: <ja...@op...> - 2004-04-20 05:30:41
|
Hey All, My suggestion is to use informative Subject: lines - it makes it much easier for others to understand what the mail is about. Harry Mangalam <hj...@ta...> writes: > > Do i need to install Bio-Perl!!!! > > Apparently. Don't for get to do a make configure each time before you > run make install. No, no, and no again - BioPerl is *not* needed by any part of genex. > > Adding mas5-short QuantitationTypeDimension ... > > /usr/local/genex/bin/qtdim-insert.pl --dbname genex --username genex --password hyde00 /home/deshmuk/genex-server/DB/curated_data/qtdim-mas5-short.xml --name=MAS-short --abbrev_name=dmas5s --version=5.0 --feat="0" --data_start_regex1=^\s+ --data_end_regex=^$ > > Can't locate Bio/MAGE.pm in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.3 /usr/local/share/perl/5.8.3 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at /usr/local/genex/bin/qtdim-insert.pl line 14. It can't find Bio::MAGE which is installed locally from the Perl/Bio-MAGE directory. There's a bug which I have fixed twice now - but apparently not committed - that skips the install of Bio-MAGE (it cd's into the *wrong* directory). I'm *really* glad that Hrishi is testing this - because these types of bugs are next to impossible for us to find - it's just not feasible to remove my entire perl distribution to test installing genex. I just committed this to r1109, do and 'svn update' and try 'make install' again. Cheers, jas. |
|
From: <ja...@op...> - 2004-12-10 16:47:02
|
Hrishikesh Deshmukh <hde...@gm...> writes: > Hi All, > > > I thought this might be useful information when writing parsers for > Affymetrix (.cel,.cdf,etc) files. > >> Subject: RE: Date: Mon, 15 Nov 2004 11:54:57 -0500 >> See Affy file format: >> > http://www.affymetrix.com/support/developer/AffxFileFormats.ZIP Hey Hrishi, Thanks, I'll keep this around. Cheers, jas. |
|
From: <hde...@gm...> - 2004-12-13 13:57:54
|
Jason, Can one do a "bulk" upload of data? I have like 200 .CEL files for the dataset! Waiting for your reply. Thanks, Hrishi |
|
From: <ja...@op...> - 2004-12-13 15:57:44
|
Hi Hrishi,
Sorry, I let this one slip.
hde...@gm... writes:
> Can one do a "bulk" upload of data?
> I have like 200 .CEL files for the dataset!
Yes.
You can either select 200 files in the GUI - maybe a bit tedious, or
you can use the command line interface. To learn how to use it type:
/usr/local/genex/bin/mbad-insert.pl --man
this spits out the documentation (you can use --help for the brief
docs if you just want a reminder what the required options are). All
the genex Perl scripts honor the --help flag, some of the more
important ones now honor --man, I convert the scripts a little at a
time to the new self-documentation system.
Anyway...
required parameters:
--username=name : the DB username to login as
--password=word : the DB password to login with
--mba_name=name : the MeasuredBioAssay name (list)
--pba_name=name : the PhysicalBioAssay name (list)
--ad_pk=pk : the ArrayDesign used
--exp_pk=pk : the primary key of the Experiment
--qtdim_pk=pk : the primary key of the QuantitationTypeDimension
--fe_sw_pk=pk : the primary key of the FeatureExtraction SW
--ro_group_id=pk : the primary key of the read-only group
--rw_group_id=pk : the primary key of the read/write group
are the required params. You need to use the genex browsing interface
to get all the pkey numbers for Experiment, ArrayDesign, QTD, FE SW,
read and write groups. The only tricky bit is --mba_name and
--pba_name. These need to be specified once for each input file - in
the same order that you list the files.
To make things easier, I just wrote a helper utility,
run-mbad-insert.pl, that reads the name and file information in from a
tab-delimited text file.
You use it like:
run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \
--ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679
here is an example input file:
/usr/local/genex/uploads/genex/200-short.txt PBA 200-short2 MBA 200-short2
/usr/local/genex/uploads/genex/201-short.txt PBA 201-short2 MBA 201-short2
/usr/local/genex/uploads/genex/202-short.txt PBA 202-short2 MBA 202-short2
spaces are allowed in the names, just not tabs. run-mbad-insert.pl is
installed and tested on genex2 in /usr/local/genex/bin.
BTW - the svn checkout directory on genex2 is:
/home/jasons/work/genex-server
in case you need to update something.
Cheers,
jas.
|
|
From: Hrishikesh D. <hde...@gm...> - 2004-12-28 16:13:46
|
Jason, I hope there were no problems in Madurai,coz of tsunami? I want to give a shot at using command line interface to load "bulk" data. Could you please explain this part: You use it like: > > run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \ > --ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679 1)What are these numbers? I understand "ad" stands for ArrayDesign but what are "ro" and "rw", meanwhile you are at it could you explain all, this i will doc them. 2)How do i get them? 3)I assume the .CEL files (they are not binary) which i have do not need to be renamed to .txt Eagerly waiting for your reply. Thanks, Hrishi Jason E. Stewart wrote: > Hi Hrishi, > > Sorry, I let this one slip. > > hde...@gm... writes: > > >>Can one do a "bulk" upload of data? >>I have like 200 .CEL files for the dataset! > > > Yes. > > You can either select 200 files in the GUI - maybe a bit tedious, or > you can use the command line interface. To learn how to use it type: > > /usr/local/genex/bin/mbad-insert.pl --man > > this spits out the documentation (you can use --help for the brief > docs if you just want a reminder what the required options are). All > the genex Perl scripts honor the --help flag, some of the more > important ones now honor --man, I convert the scripts a little at a > time to the new self-documentation system. > > Anyway... > > required parameters: > --username=name : the DB username to login as > --password=word : the DB password to login with > --mba_name=name : the MeasuredBioAssay name (list) > --pba_name=name : the PhysicalBioAssay name (list) > --ad_pk=pk : the ArrayDesign used > --exp_pk=pk : the primary key of the Experiment > --qtdim_pk=pk : the primary key of the QuantitationTypeDimension > --fe_sw_pk=pk : the primary key of the FeatureExtraction SW > --ro_group_id=pk : the primary key of the read-only group > --rw_group_id=pk : the primary key of the read/write group > > are the required params. You need to use the genex browsing interface > to get all the pkey numbers for Experiment, ArrayDesign, QTD, FE SW, > read and write groups. The only tricky bit is --mba_name and > --pba_name. These need to be specified once for each input file - in > the same order that you list the files. > > To make things easier, I just wrote a helper utility, > run-mbad-insert.pl, that reads the name and file information in from a > tab-delimited text file. > > You use it like: > > run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \ > --ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679 > > here is an example input file: > > /usr/local/genex/uploads/genex/200-short.txt PBA 200-short2 MBA 200-short2 > /usr/local/genex/uploads/genex/201-short.txt PBA 201-short2 MBA 201-short2 > /usr/local/genex/uploads/genex/202-short.txt PBA 202-short2 MBA 202-short2 > > spaces are allowed in the names, just not tabs. run-mbad-insert.pl is > installed and tested on genex2 in /usr/local/genex/bin. > > BTW - the svn checkout directory on genex2 is: > > /home/jasons/work/genex-server > > in case you need to update something. > > Cheers, > jas. > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://productguide.itmanagersjournal.com/ > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev |
|
From: <ja...@op...> - 2004-12-29 02:40:48
|
Hrishikesh Deshmukh <hde...@gm...> writes:
> I hope there were no problems in Madurai,coz of tsunami?
Actually, I've been in the Pondicherry/Auroville area for the past 6
weeks. I just left last week and went south to Nagapattnam (the huge
church at Vaillankani), and then went inland to Thanjavor. Nothing got
this far in India, so yes I am fine.
> I want to give a shot at using command line interface to load "bulk"
> data. Could you please explain this part:
>
> You use it like:
> >
> > run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \
> > --ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679
>
> 1)What are these numbers? I understand "ad" stands for ArrayDesign but
> what are "ro" and "rw", meanwhile you are at it could you explain all,
> this i will doc them.
They are documented already:
run-mbad-insert.pl --man
for verbose details
run-mbad-insert.pl --help
for brief description. All my commonly used scripts support the new
--man flag that give full details. All the rest support the --help
flag which give a brief output.
Please read the documentation and I will anwser anything that isn't
clear.
Also, please note that Perl scripts that use the Getopt::Long system
(which all the Genex scripts do) can abbreviate any command line
option down to any unique piece. This is just to save typing on the
command line. For example, '--qtdim_pk' in the above example was just
listed as '--qt' - because --qt is unabiguous to the option parser.
> 2)How do i get them?
You can either use the command line DB tool, psql, and type SQL
queries, or you can use the genex WWW table browser ("Browse by Table"
under the "Browsing" tab) - I find this convenient. Just choose the
table you want, e.g. Experiment, ArrayDesign, GroupSec, etc, then you
will be given a table of the first 100 DB entries (need to fix that),
the 'Accession Number' column is what you want to use - they are the
primary key values.
> 3)I assume the .CEL files (they are not binary) which i have do not
> need to be renamed to .txt
Correct, names do not matter.
Cheers,
jas.
|
|
From: Hrishikesh D. <hde...@gm...> - 2004-12-30 16:42:46
|
Hi Jason,
I have some questions regarding the workflow of using command line
interface to load "bulk" data.
1) I assume for the options exp,ad,dtdim, fe the primary keys are the
accession numbers which are generated once we use the GUI to insert
experiment, ad and qt-dim?!
2) Since for Affy we load CDF and thats our AD as well, so i just take
the accession number from the CDF table (there is none in the browsing
interface).
3) Correct me on this one: I have to use GUI to insert exp, ad and
qt-dim, fe and then use command line interface to load the "bulk"
files?!!! Basically create the file as shown in the example with PBA and
MBA......
Sorry the last question sounds really stupid but i want to make sure
that the workflow part can be smoothed out incase there is any need and
the same questions can go in the FAQ/docs.
Cheers,
Hrishi
Jason E. Stewart wrote:
> Hrishikesh Deshmukh <hde...@gm...> writes:
>
>
>>I hope there were no problems in Madurai,coz of tsunami?
>
>
> Actually, I've been in the Pondicherry/Auroville area for the past 6
> weeks. I just left last week and went south to Nagapattnam (the huge
> church at Vaillankani), and then went inland to Thanjavor. Nothing got
> this far in India, so yes I am fine.
>
>
>>I want to give a shot at using command line interface to load "bulk"
>>data. Could you please explain this part:
>>
>>You use it like:
>> >
>> > run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \
>> > --ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679
>>
>>1)What are these numbers? I understand "ad" stands for ArrayDesign but
>>what are "ro" and "rw", meanwhile you are at it could you explain all,
>>this i will doc them.
>
>
> They are documented already:
>
> run-mbad-insert.pl --man
>
> for verbose details
>
> run-mbad-insert.pl --help
>
> for brief description. All my commonly used scripts support the new
> --man flag that give full details. All the rest support the --help
> flag which give a brief output.
>
> Please read the documentation and I will anwser anything that isn't
> clear.
>
> Also, please note that Perl scripts that use the Getopt::Long system
> (which all the Genex scripts do) can abbreviate any command line
> option down to any unique piece. This is just to save typing on the
> command line. For example, '--qtdim_pk' in the above example was just
> listed as '--qt' - because --qt is unabiguous to the option parser.
>
>
>>2)How do i get them?
>
>
> You can either use the command line DB tool, psql, and type SQL
> queries, or you can use the genex WWW table browser ("Browse by Table"
> under the "Browsing" tab) - I find this convenient. Just choose the
> table you want, e.g. Experiment, ArrayDesign, GroupSec, etc, then you
> will be given a table of the first 100 DB entries (need to fix that),
> the 'Accession Number' column is what you want to use - they are the
> primary key values.
>
>
>>3)I assume the .CEL files (they are not binary) which i have do not
>>need to be renamed to .txt
>
>
> Correct, names do not matter.
>
> Cheers,
> jas.
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://productguide.itmanagersjournal.com/
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> https://lists.sourceforge.net/lists/listinfo/genex-dev
|
|
From: <ja...@op...> - 2004-12-31 02:05:55
|
Hrishikesh Deshmukh <hde...@gm...> writes: > 1) I assume for the options exp,ad,dtdim, fe the primary keys are the > accession numbers which are generated once we use the GUI to insert > experiment, ad and qt-dim?! Yes, correct. If this isn't clear in the documentation for the script, let me know, and suggest some wording as to how to improve it, and I will be happy to make it more clear. > 2) Since for Affy we load CDF and thats our AD as well, so i just take > the accession number from the CDF table (there is none in the browsing > interface). CDF files are just Affy's way of specifying an ArrayDesign. So there is no 'CDF' table, it is entered into the ArrayDesign table. > 3) Correct me on this one: I have to use GUI to insert exp, ad and > qt-dim, fe and then use command line interface to load the "bulk" > files?!!! Basically create the file as shown in the example with PBA > and MBA...... Correct. The FE SW must already be in the system - no one but a developer can add new ones. After the trouble I had explaining the regexp based system, I realized it was too complicated. So now, all the information is hard coded in the file parsing system. I am still (slowly) working on the generic tool to enable loading of arbitrary files, and I have only one more step to complete and I can fully test it, document it, and release it to you for more testing. Creating an Experiment is something that is done once for each, well, experiment. So once it is created you can continue to load new data into it as more hybridizations are completed in the lab. The AD and QT Dim will only be loaded once, and then re-used again and again. Once these pieces are in the DB (using the GUI tools), then you can use either the GUI loader to load multiple files (more work I believe) or the command line tool together with the load file (less work when there are many arrays to load - I believe). > Sorry the last question sounds really stupid but i want to make sure > that the workflow part can be smoothed out incase there is any need > and the same questions can go in the FAQ/docs. No problems! Happy New Year (from Chennai), jas. |
|
From: Hrishikesh D. <hde...@gm...> - 2005-01-06 17:42:59
|
Hi Jason, Happy New Year. Here is the error which i get when i try to load "bulk" data ~200 .CEL files.My guess is the error is 'coz of this particular file already in the database but i am trying to upload this file in a new experiment! Hrishi Your job is finished. The status is: ERROR The error status is: 65280 Output of the program: Using Software: MAS-CEL Using Experiment: Dec06-LUNG-Bulk-Complete Using ArrayDesign: www.affymetrix.com/ArrayDesign/HG_U95Av2-AD Dropping data indices Pre-fetching Feature Data Handled 10000 lines Handled 20000 lines Handled 30000 lines Handled 40000 lines Handled 50000 lines Handled 60000 lines Handled 70000 lines Handled 80000 lines Handled 90000 lines Handled 100000 lines Handled 110000 lines Handled 120000 lines Handled 130000 lines Handled 140000 lines Handled 150000 lines Handled 160000 lines Handled 170000 lines Handled 180000 lines Handled 190000 lines Handled 200000 lines Handled 210000 lines Handled 220000 lines Handled 230000 lines Handled 240000 lines Handled 250000 lines Handled 260000 lines Handled 270000 lines Handled 280000 lines Handled 290000 lines Handled 300000 lines Handled 310000 lines Handled 320000 lines Handled 330000 lines Handled 340000 lines Handled 350000 lines Handled 360000 lines Handled 370000 lines Handled 380000 lines Handled 390000 lines Handled 400000 lines Handled 410000 lines Copying data for MBA: CL2001031606AA.CEL into MICROARRAYSUITE_CEL Pre-fetching Feature Data Handled 10000 lines Handled 20000 lines Handled 30000 lines Handled 40000 lines Handled 50000 lines Handled 60000 lines Handled 70000 lines Handled 80000 lines Handled 90000 lines Handled 100000 lines Handled 110000 lines Handled 120000 lines Handled 130000 lines Handled 140000 lines Handled 150000 lines Handled 160000 lines Handled 170000 lines Handled 180000 lines Handled 190000 lines Handled 200000 lines Handled 210000 lines Handled 220000 lines Handled 230000 lines Handled 240000 lines Handled 250000 lines Handled 260000 lines Handled 270000 lines Handled 280000 lines Handled 290000 lines Handled 300000 lines Handled 310000 lines Handled 320000 lines Handled 330000 lines Handled 340000 lines Handled 350000 lines Handled 360000 lines Handled 370000 lines Handled 380000 lines Handled 390000 lines Handled 400000 lines Handled 410000 lines Copying data for MBA: CL2001031607AA.CEL into MICROARRAYSUITE_CEL DBD::Pg::st execute failed: ERROR: duplicate key violates unique constraint "genex_measured_bioassay_name_key" at /usr/local/share/perl/5.8.3/Bio/Genex/MeasuredBioAssay.pm line 1126. Bio::Genex::MeasuredBioAssay::insert_db: SQL=[[INSERT INTO GENEX_MEASURED_BIOASSAY (ro_gs_fk,name,rw_gs_fk,fe_sw_fk,mba_pk) VALUES ('671','CL2001031608AA.CEL','679','827','2871919')]], DBI=[[ERROR: duplicate key violates unique constraint "genex_measured_bioassay_name_key"]] at /usr/local/share/perl/5.8.3/Bio/Genex/MeasuredBioAssay.pm line 1130. /usr/local/genex/bin/mbad-insert.pl: Couldn't insert MeasuredBioAssay: CL2001031608AA.CEL, DBI=[[ERROR: duplicate key violates unique constraint "genex_measured_bioassay_name_key"]] DBD::Pg::db do failed: execute on disconnected handle at /usr/local/genex/bin/mbad-insert.pl line 401. |
|
From: <ja...@op...> - 2005-01-06 19:13:55
|
Hrishikesh Deshmukh <hde...@gm...> writes: > Happy New Year. the same. > Here is the error which i get when i try to load "bulk" data ~200 .CEL > files.My guess is the error is 'coz of this particular file already in > the database but i am trying to upload this file in a new experiment! MBA's can belong to multiple experiments - you don't need to load the same file twice - it can be reused across experiments. The MBA table declares that all MBA names must be unique. That creates a problem, it would be nice if the loader could do something nice insteading of creating an error. One thought is to just add a unique 8 character tag to the end of any MBA name that conflicts with an existing MBA - or the date or something. Or we could just remove the unique name constraint. jas. |
|
From: Hrishikesh D. <hde...@gm...> - 2005-01-06 18:42:45
|
Hi Jason, Here is the error which i get when i try to load replicates,i have double checked and this data doesn't exist in the database. I assume that somewhere the file name is used as a part of primary key, but how much of the file name is used to form the primary key?! Thanks, Hrishi Your job is finished. The status is: ERROR The error status is: 2304 Output of the program: Using Software: MAS-CEL Using Experiment: Replicates Using ArrayDesign: www.affymetrix.com/ArrayDesign/HG_U95Av2-AD Dropping data indices DBD::Pg::db do failed: ERROR: constraint "microarraysuite_cel_feature_fk_fkey" does not exist at /usr/local/genex/bin/mbad-insert.pl line 170. /usr/local/genex/bin/mbad-insert.pl: Couldn't drop indices, SQL=[[alter table MICROARRAYSUITE_CEL drop constraint MICROARRAYSUITE_CEL_feature_fk_fkey; alter table MICROARRAYSUITE_CEL drop constraint MICROARRAYSUITE_CEL_mba_fk_fkey; alter table MICROARRAYSUITE_CEL drop constraint MICROARRAYSUITE_CEL_mba_fk_key; ]], DBI=[[ERROR: constraint "microarraysuite_cel_feature_fk_fkey" does not exist]] |
|
From: Hrishikesh D. <hde...@gm...> - 2005-01-06 19:18:17
|
Hi Jason, I am attempting everything on genex2, my guess is that its running earlier version of 1725, so it may not be up-to-date!!! If you want i can update but i need step by step instructions, i have written to Harry to send the same, if you can send me the inst. i will update genex2. For the same experiment name i cannot add already loaded files(wanted to check if we could add redundancy), cannot load new files and cannot load replicates. Here is the error which i get. Your job is finished. The status is: ERROR The error status is: 2304 Output of the program: Using Software: MAS-CEL Using Experiment: Jan05-ADENO-Batch1 Using ArrayDesign: www.affymetrix.com/ArrayDesign/HG_U95Av2-AD Dropping data indices DBD::Pg::db do failed: ERROR: constraint "microarraysuite_cel_feature_fk_fkey" does not exist at /usr/local/genex/bin/mbad-insert.pl line 170. /usr/local/genex/bin/mbad-insert.pl: Couldn't drop indices, SQL=[[alter table MICROARRAYSUITE_CEL drop constraint MICROARRAYSUITE_CEL_feature_fk_fkey; alter table MICROARRAYSUITE_CEL drop constraint MICROARRAYSUITE_CEL_mba_fk_fkey; alter table MICROARRAYSUITE_CEL drop constraint MICROARRAYSUITE_CEL_mba_fk_key; ]], DBI=[[ERROR: constraint "microarraysuite_cel_feature_fk_fkey" does not exist]] Thanks, Hrishi Jason E. Stewart wrote: > Hrishikesh Deshmukh <hde...@gm...> writes: > > >>Hi Jason, >> >>Here is the error which i get when i try to use MBAD loader for >>loading data being genex_test and genex_test_curator. This should not >>happen since use of MBAD should be a simple "user" job. >> >>ERROR: ACCESS DENIED: You must be a Genex ADMIN in order to use the >>MBAD Data Loader > > > From the data loading howto: > > Then there are the required tasks for data loading. > > [snip] > > 2. The data files are loaded into the DB - requires ADMIN privelege. Required. > > The output data matrices produced by scanning the chips are > loaded into the DB using the the MBA Data Loader GUI. This will > create a single MeasuredBioAssay and PhysicalBioAssay for each > file loaded. > > This was originally a user task. Due to unforeseen performance issues > we had to use performance tweaks that require ADMIN privelege. Until > someone (else) fixes those, you have to be an admin, sorry. > > jas. |
|
From: Hrishikesh D. <hde...@gm...> - 2005-01-06 19:21:23
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Hi All, Harry & Jason: How do i check there is available space in the database to upload data? Eagerly waiting for your reply. Thanks, Hrishi |
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From: <ja...@op...> - 2005-01-07 18:24:59
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Hrishikesh Deshmukh <hde...@gm...> writes: > Harry & Jason: How do i check there is available space in the database > to upload data? The database can grow without bounds - only limited by available diskspace. To check diskspace under unix use 'df'. Cheers, jas. |
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From: Hrishikesh D. <hde...@gm...> - 2005-01-06 19:32:44
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How do i drop experiments and along with it the associated files (data files...etc.) Thanks, Hrishi Jason E. Stewart wrote: > Hrishikesh Deshmukh <hde...@gm...> writes: > > >>Happy New Year. > > > the same. > > >>Here is the error which i get when i try to load "bulk" data ~200 .CEL >>files.My guess is the error is 'coz of this particular file already in >>the database but i am trying to upload this file in a new experiment! > > > MBA's can belong to multiple experiments - you don't need to load the > same file twice - it can be reused across experiments. > > The MBA table declares that all MBA names must be unique. That creates > a problem, it would be nice if the loader could do something nice > insteading of creating an error. > > One thought is to just add a unique 8 character tag to the end of any > MBA name that conflicts with an existing MBA - or the date or > something. > > Or we could just remove the unique name constraint. > > jas. > > > ------------------------------------------------------- > The SF.Net email is sponsored by: Beat the post-holiday blues > Get a FREE limited edition SourceForge.net t-shirt from ThinkGeek. > It's fun and FREE -- well, almost....http://www.thinkgeek.com/sfshirt > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev |
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From: <hde...@gm...> - 2004-12-13 16:00:29
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The utility has been updated to genex2 or do i need to copy it to genex2 from the path that is given? Thanks, Hrishi ____________________________________________________________________ 'Life's battles don't always go to the stronger or faster man. But sooner or later the man who wins is the one who thinks he can.' -Walter D. Wintle ----- Original Message ----- From: ja...@op... (Jason E. Stewart) Date: Monday, December 13, 2004 10:54 am Subject: Re: [GeneX-dev] Re: > Hi Hrishi, > > Sorry, I let this one slip. > > hde...@gm... writes: > > > Can one do a "bulk" upload of data? > > I have like 200 .CEL files for the dataset! > > Yes. > > You can either select 200 files in the GUI - maybe a bit tedious, or > you can use the command line interface. To learn how to use it type: > > /usr/local/genex/bin/mbad-insert.pl --man > > this spits out the documentation (you can use --help for the brief > docs if you just want a reminder what the required options are). All > the genex Perl scripts honor the --help flag, some of the more > important ones now honor --man, I convert the scripts a little at a > time to the new self-documentation system. > > Anyway... > > required parameters: > --username=name : the DB username to login as > --password=word : the DB password to login with > --mba_name=name : the MeasuredBioAssay name (list) > --pba_name=name : the PhysicalBioAssay name (list) > --ad_pk=pk : the ArrayDesign used > --exp_pk=pk : the primary key of the Experiment > --qtdim_pk=pk : the primary key of the > QuantitationTypeDimension --fe_sw_pk=pk : the primary > key of the FeatureExtraction SW > --ro_group_id=pk : the primary key of the read-only group > --rw_group_id=pk : the primary key of the read/write group > > are the required params. You need to use the genex browsing interface > to get all the pkey numbers for Experiment, ArrayDesign, QTD, FE SW, > read and write groups. The only tricky bit is --mba_name and > --pba_name. These need to be specified once for each input file - in > the same order that you list the files. > > To make things easier, I just wrote a helper utility, > run-mbad-insert.pl, that reads the name and file information in > from a > tab-delimited text file. > > You use it like: > > run-mbad-insert.pl --file /tmp/file.txt --user genex --pass XXX \ > --ad 1133 --exp 1195 --qt 756 --fe 752 --ro 671 --rw 679 > > here is an example input file: > > /usr/local/genex/uploads/genex/200-short.txt PBA 200-short2 MBA > 200-short2 > /usr/local/genex/uploads/genex/201-short.txt PBA 201-short2 MBA > 201-short2 > /usr/local/genex/uploads/genex/202-short.txt PBA 202-short2 MBA > 202-short2 > > spaces are allowed in the names, just not tabs. run-mbad-insert.pl is > installed and tested on genex2 in /usr/local/genex/bin. > > BTW - the svn checkout directory on genex2 is: > > /home/jasons/work/genex-server > > in case you need to update something. > > Cheers, > jas. > |
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