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From: Junmin L. <ju...@pc...> - 2006-01-24 16:39:27
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Hi, Amruta, Ok, so the issue is that the ora_logon works in command line but not in browser. That is due to the differences of enviroments running in command line and browser. In command, you run the script as "you", I guess, in browser, you run it as "nobody" or "apache", depending on how you set it up. I am pretty sure if you "su" as "apache", then the script will fail. So there are some additional configurations missing to make sure the apache and oracle work together. Unfortuantely my knowledge stops here. Juan, can you help? In terms of the log, there is a php config file /etc/php.ini to set up how php handles the log. You should check it out. User can overwrite some of the log setting in this php.ini, like we do in current RAD-SA version, and print them out to a specific file. In your old version, the log will go to whatever file the php.ini says. ---junmin On Mon, 23 Jan 2006, Amruta Joshi wrote: > Hi, > > I had to recompile php to get the basic script running on command-line. Now > that it is failing in a browser, I suspect if some other php version is > getting called when run from browser. > Is there a way to check this? > >> 1. did you see the login page with user name and password menus when you >> start up the RAD-SA? > yes > >> I assume you did, then you saw the top saying "New users, click here", >> then you click that, and it didn't bring up anything, right? > yes > >> 2. check any output messages in the log file, which is defined in your >> webPropFile's log_file property? any useful message there? > I'm using the older RADSA. It does not have log_file property. Is there any > other way I can know what the error may be. > >> 3. from your email, i have to guess somehow the ora_logon function fails >> in your site, simply because the first "print" runs and second doesn't. > yes. > I forgot to mention that the php script spits out the correct output when > run on command line, but fails on the browser. > >> you can write it in long form: >> >> $db = "(DESCRIPTION = (ADDRESS_LIST = (ADDRESS = (PROTOCOL = TCP)(HOST = >> cbildb03.pcbi.upenn.edu)(PORT = 1521)) ) (CONNECT_DATA=(SID=...... >> $connHandle = ora_logon(DB_USER . "@$db" , DB_PASS); >> Somehow due to the way you set up the oracle, the long string works but >> short string doesn't. I guess that may be your case. > I tried using the long string. The same problem continues viz. works on > command line and fails in browser. > > thanks, > Amruta >> >> >> >> >> On Sun, 22 Jan 2006, Amruta Joshi wrote: >> >>> Hi, >>> >>> I'm trying to set up RAD StudyAnnotator using OCI. >>> I'm facing a similar problem as Juan faced earlier. >>> When I try to run user_registration.php from the web-browser, I get a >>> blank page >>> >>> I get no warning messages. In fact the function ora_logon itself fails >>> and does not return. >>> I just added 2 print statements before and after the ora_logon call in >>> include.php dbConnectionSetup function. >>> The first print is output, but not the second. Any idea where I might >>> have messed up? >>> >>> Regards, >>> Amruta >>> >>> >>> print "Trying:dbConnectionSetup"; >>> $connHandle = ora_logon(DB_USER . "@" . DB_NAME, DB_PASS); >>> print "dbConnectionSetup:ora_logon returned ".$connHandle; >>> // check if connect was successful >>> if ($connHandle <= 0) { >>> Header( "WWW-authenticate: basic realm=\"Oracle Realm\""); >>> Header( "HTTP/1.0 401 Unauthorized"); >>> printf( "Could not log into the DB.<br>"); >>> exit; >>> } >>> } >>> >>> >>> >>> ------------------------------------------------------- >>> This SF.net email is sponsored by: Splunk Inc. Do you grep through log >>> files >>> for problems? Stop! Download the new AJAX search engine that makes >>> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >>> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >>> _______________________________________________ >>> Gusdev-rad-issues mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues >>> > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Amruta J. <am...@st...> - 2006-01-23 23:31:17
|
Hi, I had to recompile php to get the basic script running on command-line. Now that it is failing in a browser, I suspect if some other php version is getting called when run from browser. Is there a way to check this? > 1. did you see the login page with user name and password menus when you > start up the RAD-SA? yes > I assume you did, then you saw the top saying "New users, click here", > then you click that, and it didn't bring up anything, right? yes > 2. check any output messages in the log file, which is defined in your > webPropFile's log_file property? any useful message there? I'm using the older RADSA. It does not have log_file property. Is there any other way I can know what the error may be. > 3. from your email, i have to guess somehow the ora_logon function fails > in your site, simply because the first "print" runs and second doesn't. yes. I forgot to mention that the php script spits out the correct output when run on command line, but fails on the browser. > you can write it in long form: > > $db = "(DESCRIPTION = (ADDRESS_LIST = (ADDRESS = (PROTOCOL = TCP)(HOST = > cbildb03.pcbi.upenn.edu)(PORT = 1521)) ) (CONNECT_DATA=(SID=...... > $connHandle = ora_logon(DB_USER . "@$db" , DB_PASS); > Somehow due to the way you set up the oracle, the long string works but > short string doesn't. I guess that may be your case. I tried using the long string. The same problem continues viz. works on command line and fails in browser. thanks, Amruta > > > > > On Sun, 22 Jan 2006, Amruta Joshi wrote: > >> Hi, >> >> I'm trying to set up RAD StudyAnnotator using OCI. >> I'm facing a similar problem as Juan faced earlier. >> When I try to run user_registration.php from the web-browser, I get a >> blank page >> >> I get no warning messages. In fact the function ora_logon itself fails >> and does not return. >> I just added 2 print statements before and after the ora_logon call in >> include.php dbConnectionSetup function. >> The first print is output, but not the second. Any idea where I might >> have messed up? >> >> Regards, >> Amruta >> >> >> print "Trying:dbConnectionSetup"; >> $connHandle = ora_logon(DB_USER . "@" . DB_NAME, DB_PASS); >> print "dbConnectionSetup:ora_logon returned ".$connHandle; >> // check if connect was successful >> if ($connHandle <= 0) { >> Header( "WWW-authenticate: basic realm=\"Oracle Realm\""); >> Header( "HTTP/1.0 401 Unauthorized"); >> printf( "Could not log into the DB.<br>"); >> exit; >> } >> } >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep through log >> files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 >> _______________________________________________ >> Gusdev-rad-issues mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues >> |
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From: Junmin L. <ju...@pc...> - 2006-01-23 16:33:10
|
Hi, Amruta, Here are my questions and suggestions: 1. did you see the login page with user name and password menus when you start up the RAD-SA? I assume you did, then you saw the top saying "New users, click here", then you click that, and it didn't bring up anything, right? 2. check any output messages in the log file, which is defined in your webPropFile's log_file property? any useful message there? 3. from your email, i have to guess somehow the ora_logon function fails in your site, simply because the first "print" runs and second doesn't. so this is the function: ora_logon(DB_USER . "@" . DB_NAME, DB_PASS) a. can you check if the "DB_USER" and "DB_NAME" can connect to db by using sqlplus? b. you have correct "oracle_home" set up? c. please write up a small test script to connect to your oracle db using the ora_logon() function. d. in terms of the ora_logon(), you can write it in short/simple form like we does in RADSA, or you can write it in long form: $db = "(DESCRIPTION = (ADDRESS_LIST = (ADDRESS = (PROTOCOL = TCP)(HOST = cbildb03.pcbi.upenn.edu)(PORT = 1521)) ) (CONNECT_DATA=(SID=...... $connHandle = ora_logon(DB_USER . "@$db" , DB_PASS); Somehow due to the way you set up the oracle, the long string works but short string doesn't. I guess that may be your case. Please check all of the options and let me know how they go. Thanks, ----junmin On Sun, 22 Jan 2006, Amruta Joshi wrote: > Hi, > > I'm trying to set up RAD StudyAnnotator using OCI. > I'm facing a similar problem as Juan faced earlier. > When I try to run user_registration.php from the web-browser, I get a blank > page > > I get no warning messages. In fact the function ora_logon itself fails and > does not return. > I just added 2 print statements before and after the ora_logon call in > include.php dbConnectionSetup function. > The first print is output, but not the second. Any idea where I might have > messed up? > > Regards, > Amruta > > > print "Trying:dbConnectionSetup"; > $connHandle = ora_logon(DB_USER . "@" . DB_NAME, DB_PASS); > print "dbConnectionSetup:ora_logon returned ".$connHandle; > // check if connect was successful > if ($connHandle <= 0) { > Header( "WWW-authenticate: basic realm=\"Oracle Realm\""); > Header( "HTTP/1.0 401 Unauthorized"); > printf( "Could not log into the DB.<br>"); > exit; > } > } > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=103432&bid=230486&dat=121642 > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Trish W. <wh...@pc...> - 2006-01-23 13:03:15
|
> I'm trying to set up RAD StudyAnnotator using OCI. > I'm facing a similar problem as Juan faced earlier. > When I try to run user_registration.php from the web-browser, I get a blank > page > > I get no warning messages. In fact the function ora_logon itself fails and > does not return. > I just added 2 print statements before and after the ora_logon call in > include.php dbConnectionSetup function. > The first print is output, but not the second. Any idea where I might have > messed up? If I recall correctly, part of the problem was that there was no data in the core.projectinfo and core.groupinfo tables. Have you loaded those tables yet? Trish |
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From: Amruta J. <am...@st...> - 2006-01-23 02:56:37
|
Hi,
I'm trying to set up RAD StudyAnnotator using OCI.
I'm facing a similar problem as Juan faced earlier.
When I try to run user_registration.php from the web-browser, I get a blank
page
I get no warning messages. In fact the function ora_logon itself fails and
does not return.
I just added 2 print statements before and after the ora_logon call in
include.php dbConnectionSetup function.
The first print is output, but not the second. Any idea where I might have
messed up?
Regards,
Amruta
print "Trying:dbConnectionSetup";
$connHandle = ora_logon(DB_USER . "@" . DB_NAME, DB_PASS);
print "dbConnectionSetup:ora_logon returned ".$connHandle;
// check if connect was successful
if ($connHandle <= 0) {
Header( "WWW-authenticate: basic realm=\"Oracle Realm\"");
Header( "HTTP/1.0 401 Unauthorized");
printf( "Could not log into the DB.<br>");
exit;
}
}
|
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From: Elisabetta M. <man...@pc...> - 2006-01-06 18:02:08
|
Juan Carlos Perin has installed the RADSA 2.0.0 at CHOP and has kindly provided detailed notes of what he did from start to finish (including GUS installation) to accomplish this goal. His notes can be useful also to those installing RADSA 2.1.0. I've posted them at http://www.cbil.upenn.edu/downloads/RAD/ as well. (JCPerin_InstallingRADSA.doc). Thanks Juan! Elisabetta |
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From: Elisabetta M. <man...@pc...> - 2006-01-06 14:54:23
|
(Apologies if you receive this email more than once, it is being mailed to various mailing lists.) Release 2.1.0 of the RADSA is now available at http://www.cbil.upenn.edu/downloads/RAD/. This is compatible with GUS 3.5. The README file included in the tarball contains instructions both for a fresh install and for upgrading from RADSA 2.0.0. As compared to 2.0.0 this new release contains improved code for the user_registration and ontology entry search forms, and other minor modifications. Elisabetta |
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From: Junmin L. <ju...@pc...> - 2005-12-21 20:14:18
|
Interesting, could you send the whole error message? Thanks, ---junmin On Wed, 21 Dec 2005, Juan Carlos Perin wrote: > Loading RADSAhelp.tab file into radsa.radsahelp table using sqlldr fails to > load all records. First error was that IS_MANDATORY is set to VARCHAR(4) > when several of the fields in the tab file are size 6. I also get errors > about the size of DEFINITION. I increase this size to 2000, and increase > IS_MANDATORY to 6, and I am able to load 233 of the 274 records. Previously > only 54 loaded. The IS_MANDATORY error is gone but still get DEFINTION size > limit errors. I'm looking at the 'bad' rows and am sure that the > DEFINITIONS are not too long, so I assume there is a problem with special > characters perhaps. (quotes, slashes or double-quotes). My control file for > sqlldr looks like this: > > LOAD DATA > INFILE 'RADSAhelp.tab' > APPEND INTO table RADSA.RADSAHELP > FIELDS TERMINATED BY ' ' > trailing nullcols > ( > RADSA_HELP_ID, > FORM_NAME, > FIELD_NAME, > ATTRIBUTE_NAME, > IS_MANDATORY, > DEFINITION, > EXAMPLES > ) > > > This is on Oracle 10g. Perhaps my syntax needs something else for the > control file? > > Juan > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Juan C. P. <bi...@ge...> - 2005-12-21 20:10:27
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Loading RADSAhelp.tab file into radsa.radsahelp table using sqlldr fails to load all records. First error was that IS_MANDATORY is set to VARCHAR(4) when several of the fields in the tab file are size 6. I also get errors about the size of DEFINITION. I increase this size to 2000, and increase IS_MANDATORY to 6, and I am able to load 233 of the 274 records. Previously only 54 loaded. The IS_MANDATORY error is gone but still get DEFINTION size limit errors. I'm looking at the 'bad' rows and am sure that the DEFINITIONS are not too long, so I assume there is a problem with special characters perhaps. (quotes, slashes or double-quotes). My control file for sqlldr looks like this: LOAD DATA INFILE 'RADSAhelp.tab' APPEND INTO table RADSA.RADSAHELP FIELDS TERMINATED BY ' ' trailing nullcols ( RADSA_HELP_ID, FORM_NAME, FIELD_NAME, ATTRIBUTE_NAME, IS_MANDATORY, DEFINITION, EXAMPLES ) This is on Oracle 10g. Perhaps my syntax needs something else for the control file? Juan |
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From: Junmin L. <ju...@pc...> - 2005-12-14 20:28:35
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This plugin doesn't support loading elementResult for affy data. It only load compositeElementResult for affy data. I think it is current way we use RAD in cbil. --junmin On Wed, 14 Dec 2005, Elisabetta Manduchi wrote: > > Hi Sucheta, > the first thing you need to check is that you are complying with the > documentation for this plugin, especially in the input data_file format. > HTML documentation can be generated by running the plugin with just the > --helpHTML option. > If you are using GUS 3.5 this plugin is named LoadArrayResults and > documentation is also available at > https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/doc/LoadArrayResults.html > The usage of this plugin didn't change much from 3.0 to 3.5. > > Now, it looks like you are trying to simultaenously load both the .CEL and > the MAS 5 probe set results. I'm not sure the plugin can handle this, that > is, you might need to load separately the results for the CEL and the MAS 5 > probeset quantifications (note that they should refer to different > quantifications). But I'll let JUNMIN (here cc-ed) confirm on this, as he is > the author of this plugin. I see that the plugin documentation is not clear > on this point. Here we typically load only the probe_set results in the db > (e.g. AffymetrixMAS4 or AffymetrixMAS5 or RMAExpress views). For the .cel > files we simply create a quantification in RAD.Quantification for the .cel > results with the uri pointing to where we hold the .CEL file in our > filesystem. > If loading only the probeset results, the typical header of the data_file > should be: > name signal detection detection_p_value > > (and optionally also stat_pairs and stat_pairs_used) > tab separated, no commas. > > In any case, should you still have problems after checking the data format, > please email Junmin directly. Make sure you include in your email: GUS > version you are using, command line, top portion of the data_file, any error > message you get, and description of the problem > > Elisabetta > P.S. Note that we also have a batch result loader that works for MAS5 probe > set results loading them in batch. In GUS 3.5 the name of this > plugin is GUS::Community::Plugin::LoadBatchArrayResults. > > --- > > On Wed, 14 Dec 2005, Sucheta Tripathy wrote: > >> Hi Elisabetta, >> >> I am using arrayresultloader to upload the array data into GUS. It does a >> decent job but crashes inbetween without giving a proper error message. >> Could it be due to my computer related issues. >> >> Also when I have a line having data such as: >> >> x_position, y_position, mean, stdv, npixels, name, >> detection, detection_p_value, signal >> 621 275 76.0 10.5 25 >> PsAffx.C17000127_at A 0.111572 10.95974 >> >> But when I upload the data it changes the fields into: >> >> Debug 621 275 44.0 7.5 25 PsAffx.C17000127_at A 0.24 >> 6094 10.821429 >> >> and says mean 44.0 and stdv 7.5 etc. >> >> Is there a reason why the values are changed? >> >> Thanks >> >> Sucheta >> >> >> >> ------------------------------------------------------- >> This SF.net email is sponsored by: Splunk Inc. Do you grep through log >> files >> for problems? Stop! Download the new AJAX search engine that makes >> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! >> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click >> _______________________________________________ >> Gusdev-rad-issues mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues >> > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Junmin L. <ju...@pc...> - 2005-12-14 19:54:15
|
Hi, Sucheta, > I am using arrayresultloader to upload the array data into GUS. It does a > decent job but crashes inbetween without giving a proper error message. Could > it be due to my computer related issues. That could be due to the memory size in your machine. > > Also when I have a line having data such as: > > x_position, y_position, mean, stdv, npixels, name, > detection, detection_p_value, signal > 621 275 76.0 10.5 25 > PsAffx.C17000127_at A 0.111572 10.95974 > > But when I upload the data it changes the fields into: > > Debug 621 275 44.0 7.5 25 PsAffx.C17000127_at A 0.24 > 6094 10.821429 Can you tell me "which fields" they are? > and says mean 44.0 and stdv 7.5 etc. > I don't understand the above setence. Could you explain? Also when you report the bugs or issues of the plugin, please provide the following information: 1. the complete ga command you run. 2. the portion of the data file your run with, e.g., the first 100 lines. 3. the output message from the plugin. 4. what happend when you run the plugin in "non-commit" model 5. what happend when you using the "--testnumber" option of the plugin. That will help me to solve your issues. And I will suggest you always run the plugin with the above point 4 and 5 first to test it against your data file. --junmin |
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From: Elisabetta M. <man...@pc...> - 2005-12-14 19:46:16
|
Hi Sucheta, the first thing you need to check is that you are complying with the documentation for this plugin, especially in the input data_file format. HTML documentation can be generated by running the plugin with just the --helpHTML option. If you are using GUS 3.5 this plugin is named LoadArrayResults and documentation is also available at https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/doc/LoadArrayResults.html The usage of this plugin didn't change much from 3.0 to 3.5. Now, it looks like you are trying to simultaenously load both the .CEL and the MAS 5 probe set results. I'm not sure the plugin can handle this, that is, you might need to load separately the results for the CEL and the MAS 5 probeset quantifications (note that they should refer to different quantifications). But I'll let JUNMIN (here cc-ed) confirm on this, as he is the author of this plugin. I see that the plugin documentation is not clear on this point. Here we typically load only the probe_set results in the db (e.g. AffymetrixMAS4 or AffymetrixMAS5 or RMAExpress views). For the .cel files we simply create a quantification in RAD.Quantification for the .cel results with the uri pointing to where we hold the .CEL file in our filesystem. If loading only the probeset results, the typical header of the data_file should be: name signal detection detection_p_value (and optionally also stat_pairs and stat_pairs_used) tab separated, no commas. In any case, should you still have problems after checking the data format, please email Junmin directly. Make sure you include in your email: GUS version you are using, command line, top portion of the data_file, any error message you get, and description of the problem Elisabetta P.S. Note that we also have a batch result loader that works for MAS5 probe set results loading them in batch. In GUS 3.5 the name of this plugin is GUS::Community::Plugin::LoadBatchArrayResults. --- On Wed, 14 Dec 2005, Sucheta Tripathy wrote: > Hi Elisabetta, > > I am using arrayresultloader to upload the array data into GUS. It does a > decent job but crashes inbetween without giving a proper error message. > Could it be due to my computer related issues. > > Also when I have a line having data such as: > > x_position, y_position, mean, stdv, npixels, name, > detection, detection_p_value, signal > 621 275 76.0 10.5 25 > PsAffx.C17000127_at A 0.111572 10.95974 > > But when I upload the data it changes the fields into: > > Debug 621 275 44.0 7.5 25 PsAffx.C17000127_at A > 0.24 > 6094 10.821429 > > and says mean 44.0 and stdv 7.5 etc. > > Is there a reason why the values are changed? > > Thanks > > Sucheta > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log > files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Sucheta T. <su...@vb...> - 2005-12-14 18:56:40
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Hi Elisabetta, I am using arrayresultloader to upload the array data into GUS. It does a decent job but crashes inbetween without giving a proper error message. Could it be due to my computer related issues. Also when I have a line having data such as: x_position, y_position, mean, stdv, npixels, name, detection, detection_p_value, signal 621 275 76.0 10.5 25 PsAffx.C17000127_at A 0.111572 10.95974 But when I upload the data it changes the fields into: Debug 621 275 44.0 7.5 25 PsAffx.C17000127_at A 0.24 6094 10.821429 and says mean 44.0 and stdv 7.5 etc. Is there a reason why the values are changed? Thanks Sucheta |
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From: Elisabetta M. <man...@pc...> - 2005-11-30 16:54:57
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As an addition, the user registration form (and mail_user_registration and modifyPassword) is mostly to allow external users to submit an account request. This form itself doesn't enter data into the db but only creates some xml, because before creating a new user account it is assumed that some manual verification and approval is needed by those maintaining the db instance, in your case you. (The rest of the RADSA forms actually enter data in the db). Typically the xml produced by the mail_user_registration form will necessitate manual modifications by the db maintainers because of this. In the upcoming RADSA 2.1.0 release (scheduled for January) the code of this form has been trimmed and modified. If you are creating accounts just for yourself to use the RADSA, you are better off just creating the xml directly and loading it via the plugin GUS::Supported::Plugin::LoadGusXml. For a given user account you can create nested xml to create the contact in SRes.Contact, its child in Core.UserInfo and the children of the latter in Core.UserProject and Core.UserGroup to link the user to whatever projects and groups they belong. (Project and Groups that you guys want can be created previously using LoadGusXml: we typically create a "Testing" project and "Testing" group in addition to our regular projects and group, and all data entered under these project/group is considered temporary/test only.) If you nest the UserProject and UserGroup xml within the UserInfo xml and the latter within the Contact xml, LoadGusXml will submit all in one transaction and create the appropriate foreign keys. Finally, you should create an entry in Core.ProjectInfo whose name is 'RAD' and then use the Rad.ProjectLink table to link to this 'RAD' project all contacts and other projects and groups that refer or utilize RAD. Elisabetta --- On Wed, 30 Nov 2005, Junmin Liu wrote: > Hi, Juan, > >> directly. When I run on the command line, the web pages seem to work just >> fine, and I see all the HTML and javascript spit out to STDOUT, BUT I get >> the following error in my error log: >> >> [30-Nov-2005 12:08:37] PHP Warning: ora_getcolumn(): Ora_Fetch failed >> (ORA-01002: fetch out of sequence -- while processing OCI function >> OFETCH/OFEN) in /usr/local/apache2/htdocs/misc/user_registration.php on >> line 153 >> > > This will be due to the bug in the code, ora_fetch will return a record > within the results, most likely the code assumes it return many records and > try to loop through it, while the correponding table you have in your > instance is empty, so the cursoe has o record. Then you got the "out of > sequence". > > >> I assume this has something to do with the issues in compiling PHP with >> OCI8 >> and with oracle. >> >> When I try to run user_registration.php from the web-browser, I get a blank >> page, and I get the following in the error log: >> >> [30-Nov-2005 12:10:22] PHP Warning: >> dbConnectionSetup(/home/oracle/RADSA_2.0.0/db-include.inc) [<a >> href='function.dbConnectionSetup'>function.dbConnectionSetup</a>]: >> failed to open stream: Permission denied in >> /usr/local/apache2/htdocs/include/php/db.inc on line 6 >> >> [30-Nov-2005 12:10:22] PHP Fatal error: dbConnectionSetup() [<a >> href='function.require'>function.require</a>]: Failed opening required >> '/home/oracle/RADSA_2.0.0/db-include.inc' >> ---(include_path='.:/usr/local/apache2/htdocs/include/php/:./include/php:.. >> ----/include/php') in /usr/local/apache2/htdocs/include/php/db.inc on line >> 6 > > what is the permission for this file. You should let it owned by apache, set > it to 700 for security reason. > > /home/oracle/RADSA_2.0.0/db-include.inc > > ---junmin > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Junmin L. <ju...@pc...> - 2005-11-30 16:21:16
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Hi, Juan, > directly. When I run on the command line, the web pages seem to work just > fine, and I see all the HTML and javascript spit out to STDOUT, BUT I get > the following error in my error log: > > [30-Nov-2005 12:08:37] PHP Warning: ora_getcolumn(): Ora_Fetch failed > (ORA-01002: fetch out of sequence -- while processing OCI function > OFETCH/OFEN) in /usr/local/apache2/htdocs/misc/user_registration.php on > line 153 > This will be due to the bug in the code, ora_fetch will return a record within the results, most likely the code assumes it return many records and try to loop through it, while the correponding table you have in your instance is empty, so the cursoe has o record. Then you got the "out of sequence". > I assume this has something to do with the issues in compiling PHP with OCI8 > and with oracle. > > When I try to run user_registration.php from the web-browser, I get a blank > page, and I get the following in the error log: > > [30-Nov-2005 12:10:22] PHP Warning: > dbConnectionSetup(/home/oracle/RADSA_2.0.0/db-include.inc) [<a > href='function.dbConnectionSetup'>function.dbConnectionSetup</a>]: > failed to open stream: Permission denied in > /usr/local/apache2/htdocs/include/php/db.inc on line 6 > > [30-Nov-2005 12:10:22] PHP Fatal error: dbConnectionSetup() [<a > href='function.require'>function.require</a>]: Failed opening required > '/home/oracle/RADSA_2.0.0/db-include.inc' > ---(include_path='.:/usr/local/apache2/htdocs/include/php/:./include/php:.. > ----/include/php') in /usr/local/apache2/htdocs/include/php/db.inc on line 6 what is the permission for this file. You should let it owned by apache, set it to 700 for security reason. /home/oracle/RADSA_2.0.0/db-include.inc ---junmin |
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From: Juan C. P. <bi...@ge...> - 2005-11-30 16:05:33
|
I'm testing out the web pages that were created, and I'm not getting pages
to load in the browsers properly. I have edited php.ini to allow registered
globals for the cookies. I enabled php in apache and have ORACLE_HOME set.
I had to edit my user_registration.php file because it was calling require()
which was not set to the right db-include for me, so I had to specify it
directly. When I run on the command line, the web pages seem to work just
fine, and I see all the HTML and javascript spit out to STDOUT, BUT I get
the following error in my error log:
[30-Nov-2005 12:08:37] PHP Warning: ora_getcolumn(): Ora_Fetch failed
(ORA-01002: fetch out of sequence -- while processing OCI function
OFETCH/OFEN) in /usr/local/apache2/htdocs/misc/user_registration.php on
line 153
I assume this has something to do with the issues in compiling PHP with OCI8
and with oracle.
When I try to run user_registration.php from the web-browser, I get a blank
page, and I get the following in the error log:
[30-Nov-2005 12:10:22] PHP Warning:
dbConnectionSetup(/home/oracle/RADSA_2.0.0/db-include.inc) [<a
href='function.dbConnectionSetup'>function.dbConnectionSetup</a>]:
failed to open stream: Permission denied in
/usr/local/apache2/htdocs/include/php/db.inc on line 6
[30-Nov-2005 12:10:22] PHP Fatal error: dbConnectionSetup() [<a
href='function.require'>function.require</a>]: Failed opening required
'/home/oracle/RADSA_2.0.0/db-include.inc'
---(include_path='.:/usr/local/apache2/htdocs/include/php/:./include/php:..
----/include/php') in /usr/local/apache2/htdocs/include/php/db.inc on line 6
My permissions are 777 for all these include files and directories, so I
don't think the web user is having issues with permissions. I don't know
what else could be necessarily different between the apache user and myself
(as 'oracle' user), unless I'm not realizing some other environment
variables set improperly or not set at all.
Juan
|
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From: Trish W. <wh...@pc...> - 2005-11-29 01:50:16
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After further discussion it was noted that of either of the url possibilities to use, the download_url is the better choice. The plugin and documentation have been updated to reflect this. Trish |
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From: Elisabetta M. <man...@pc...> - 2005-11-28 19:49:58
|
Hi Juan, at CBIL we use the CV described at http://www.cbil.upenn.edu/anatomy.php3 for anatomy. We have just posted a dump of our Anatomy file from 10/05/05 at http://www.cbil.upenn.edu/downloads/Ontologies/ Elisabetta --- On Mon, 28 Nov 2005, Juan Carlos Perin wrote: > Because I'm new to this, I'm writing to ask for recommendations on the > preferred ontologies for inserting into these tables? I'd like to stick to > the ontologies that are used at Penn. Thanks! > > Juan > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Elisabetta M. <man...@pc...> - 2005-11-28 19:28:03
|
Juan,
sorry, it looks like the sample webPropFile file in the tarball is missing
some lines, namely:
log_file={the full path for the RADSA log file}
queryFile={the full path to the query.cfg file}
annotatorlog_file={the full path for the session log file}
session_file={the directory where the session files should be stored}
I'll post an updated version of a sample webPropFile at the RAD download
site shortly.
Elisabetta
---
On Mon, 28 Nov 2005, Juan Carlos Perin wrote:
> With this:
>
> sudo build RAD/StudyAnnotator webinstall -append -webPropFile
> /home/oracle/GUS/project_home/RAD/studyAnnotatorWebConfig.prop
>
> I get:
>
> BUILD FAILED
> /home/oracle/GUS/project_home/install/build.xml:51: The following error
> occurred while executing this line:
> /home/oracle/GUS/project_home/RAD/build.xml:142: property "log_file" was not
> found in /home/oracle/GUS/project_home/RAD/studyAnnotatorWebConfig.prop
>
> Total time: 1 second
>
> Should there be another reference in the .prop file?
>
> Juan
>
>
>
>
> -------------------------------------------------------
> This SF.net email is sponsored by: Splunk Inc. Do you grep through log files
> for problems? Stop! Download the new AJAX search engine that makes
> searching your log files as easy as surfing the web. DOWNLOAD SPLUNK!
> http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click
> _______________________________________________
> Gusdev-rad-issues mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues
>
|
|
From: Juan C. P. <bi...@ge...> - 2005-11-28 19:14:56
|
With this: sudo build RAD/StudyAnnotator webinstall -append -webPropFile /home/oracle/GUS/project_home/RAD/studyAnnotatorWebConfig.prop I get: BUILD FAILED /home/oracle/GUS/project_home/install/build.xml:51: The following error occurred while executing this line: /home/oracle/GUS/project_home/RAD/build.xml:142: property "log_file" was not found in /home/oracle/GUS/project_home/RAD/studyAnnotatorWebConfig.prop Total time: 1 second Should there be another reference in the .prop file? Juan |
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From: Juan C. P. <bi...@ge...> - 2005-11-28 18:35:01
|
Because I'm new to this, I'm writing to ask for recommendations on the preferred ontologies for inserting into these tables? I'd like to stick to the ontologies that are used at Penn. Thanks! Juan |
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From: Junmin L. <ju...@pc...> - 2005-11-23 22:12:03
|
Hi, Trish, Sorry I have to disagree with the way the plugin handles this. I have filed a bug in the tracker: https://www.cbil.upenn.edu/tracker/show_bug.cgi?id=239 Please see the bug report for the reasons. ---junmin On Wed, 23 Nov 2005, Trish Whetzel wrote: >> The query fails because its looking at id_url in >> sres.externaldatabaserelease and trying to match the URL with this ID which >> is set to a number not the hard-coded URL above. So loading >> StudyOntologyEntrydum_1.0.0.tab fails. I don't know if this is my error. >> I >> could either forcefully change the value of url_id to http://mged.etc... Or >> change the hard coded value in the module to the associated number for the >> external database release value. I don't see a way to specify this value >> when inserting the external database values. > Check that the id_url is specified for the MGED Ontology entry in > SRes.ExternalDatabaseRelease. The documentation, > README_StudyOntologyEntryDump_1.0.0, has been updated with this point. > > Trish > > > ------------------------------------------------------- > This SF.net email is sponsored by: Splunk Inc. Do you grep through log files > for problems? Stop! Download the new AJAX search engine that makes > searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! > http://ads.osdn.com/?ad_id=7637&alloc_id=16865&op=click > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
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From: Trish W. <wh...@pc...> - 2005-11-23 21:15:07
|
> The query fails because its looking at id_url in > sres.externaldatabaserelease and trying to match the URL with this ID which > is set to a number not the hard-coded URL above. So loading > StudyOntologyEntrydum_1.0.0.tab fails. I don't know if this is my error. I > could either forcefully change the value of url_id to http://mged.etc... Or > change the hard coded value in the module to the associated number for the > external database release value. I don't see a way to specify this value > when inserting the external database values. Check that the id_url is specified for the MGED Ontology entry in SRes.ExternalDatabaseRelease. The documentation, README_StudyOntologyEntryDump_1.0.0, has been updated with this point. Trish |
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From: Josef J. <ju...@cs...> - 2005-11-22 23:00:43
|
Elisabetta Manduchi <man...@pc...> writes: > > [...] > Note that there are other measures in the typical GenePix output file that > have not been put into the view intentionally, as they can be derived from > those already in, I noticed; yes, there is a lot of redundant information in GenePix files. > but I don't think this is the case for X and Y. > A note: I think that X and Y might be assay-dependent, in which case they > do indeed belong to a view of RAD.ElementResultImp. If however they were > the same for all assays on the same array they they should be placed in > the RAD.Spot view of ElementImp (e.g. the ShortOligo view has these for > Affy). I think though that it's the former case, can you confirm? It is the former case, these values are Assay dependent, they cannot be derived from other columns, and therefore this is a bug and these columns must be added to the table. I will put something in the bug tracker. Thanks, Josef |
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From: Elisabetta M. <man...@pc...> - 2005-11-22 22:36:23
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Hi Josef, if these are important to you they can be added to the view (you might=20 want to file a bug on the tracker so we can keep it in mind for future=20 releases). I see that the ArrayVision view of ElementResultImp, for=20 example, has these. Note that there are other measures in the typical GenePix output file that= =20 have not been put into the view intentionally, as they can be derived from= =20 those already in, but I don't think this is the case for X and Y. A note: I think that X and Y might be assay-dependent, in which case they= =20 do indeed belong to a view of RAD.ElementResultImp. If however they were=20 the same for all assays on the same array they they should be placed in=20 the RAD.Spot view of ElementImp (e.g. the ShortOligo view has these for=20 Affy). I think though that it's the former case, can you confirm? Elisabetta --- On Tue, 22 Nov 2005, Josef Jurek wrote: > > > In looking over the several typical output files of GenePix, > I see that most of the important values of these files map > to fields of the RAD.GenePixElementResult view: > > GenePix RAD table > > X ? > Y ? > Dia. RAD.GenePixElementResult.SPOT_DIAMETER > F635 Median RAD.GenePixElementResult.FOREGROUND_MEDIAN > F635 Mean RAD.GenePixElementResult.FOREGROUND_MEAN > F635 SD RAD.GenePixElementResult.FOREGROUND_SD > B635 Median RAD.GenePixElementResult.BACKGROUND_MEDIAN > B635 Mean RAD.GenePixElementResult.BACKGROUND_MEAN > B635 SD RAD.GenePixElementResult.BACKGROUND_SD > % > B635+1SD RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_= ONE_SD > % > B635+2SD RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_= TWO_SDS > F635 % Sat. RAD.GenePixElementResult.PERCENT_FOREGROUND_SA= TURATED > ... ... > F Pixels RAD.GenePixElementResult.NUM_FOREGROUND_PIXELS > B Pixels RAD.GenePixElementResult.NUM_BACKGROUND_PIXELS > Circularity RAD.GenePixElementResult.CIRCULARITY > > > however as far as I can tell, there is no place in the view to put > the values of the columns that are labeled "X" and "Y" from a GenePix > output file. GenePix describes these values as follows > > X the X-coordinate in =C2=B5m of the center of the feature-indicat= or associated with > the feature, where (0,0) is the top left of the image. > > Y the Y-coordinate in =C2=B5m of the center of the feature-indicat= or associated with > the feature, where (0,0) is the top left of the image. > > This is important information that we do not want to toss away. > Is this an oversight, or have I missed something? > > I hope columns for these two values can be added to this table/view. > We will have to go a head an this columns in our locally installed > version of RAD anyways, as we need this. > > Thanks Josef > > > > > Josef Jurek > > Daphne Preuss Laboratory > Molecular Genetics and Cell Biology > The University of Chicago > ju...@cs... > > voice: (773) 834-3985 > fax: (773) 702-6648 > > > > ------------------------------------------------------- > This SF.Net email is sponsored by the JBoss Inc. Get Certified Today > Register for a JBoss Training Course. Free Certification Exam > for All Training Attendees Through End of 2005. For more info visit: > http://ads.osdn.com/?ad_id=3D7628&alloc_id=3D16845&op=3Dclick > _______________________________________________ > Gusdev-rad-issues mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-rad-issues > |
