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[GeneX-dev] Re: [Genex-users] Re:
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From: Harry M. <hj...@ta...> - 2004-04-19 21:55:24
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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>> |
