Discussion:
error with reporter list
(too old to reply)
RIGOR,PAUL MACARAEG
2004-06-18 16:40:02 UTC
Permalink
Hi all,

I'm having a problem adding a raw results file after the "add scan" step.
I'm using base version: 1.2.11. The error is:

Error on line 11: Unable to create new reporter '(+)Pro25G-03'
Operation aborted

Steps to reproduce the error:
1) select Hybrization
2) select Scan
3) under Raw data sets, select "upload result file"
4) choose result file format
5) clicking on continue shows the error...

Thanks,
Paul
Paul Rigor
2004-06-23 13:12:40 UTC
Permalink
Hi all,

Has anyone run into a problem when trying to add a new reporter?

The SETUP:
A) First of all, here's my server's setup. Base 1.2.11, MySql 3, Apache
2, Fedora Core1.

B) Second is the base custom sql column setup. For the sql (e.g.,
baseroot/sql/base_mysql.sql), I've added extra columns at the end of
both the 1) Reporter and 2) RawBioAssayData tables. I've ensured that
I've used correct syntax in adding these columns.

C) Third is the base html/php changes. I've included the corresponding
array calls (from the sql changes) in the following files in
baseroot/include/local/raw_columns.inc.php AND
baseroot/include/local/reporter_columns.inc.php. I've also entered
these new array calls with correct syntax.

The PROBLEM:

I've attached a previous email regarding an error that occurs when
trying to add a new reporter in base. The "(+)Pro25G-03" is just a data
below the data header. Am I supposed to use the line which contains the
data header while setting up the reporters in base?

Thanks!!
Paul Rigor
Post by RIGOR,PAUL MACARAEG
Hi all,
I'm having a problem adding a raw results file after the "add scan" step.
Error on line 11: Unable to create new reporter '(+)Pro25G-03'
Operation aborted
1) select Hybrization
2) select Scan
3) under Raw data sets, select "upload result file"
4) choose result file format
5) clicking on continue shows the error...
Thanks,
Paul
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Carl Troein
2004-06-27 23:03:04 UTC
Permalink
Post by RIGOR,PAUL MACARAEG
I'm having a problem adding a raw results file after the "add scan" step.
Error on line 11: Unable to create new reporter '(+)Pro25G-03'
Operation aborted
1) select Hybrization
2) select Scan
3) under Raw data sets, select "upload result file"
4) choose result file format
5) clicking on continue shows the error...
Hmm... it would help to see the error message logged to the PHP (or
Apache) error log, but I think can guess what it is. Unless it's
something as trivial as 'disk full' or 'access denied' (or as nasty
as a corrupted file), it's a duplicate key error of some kind. I've
looked at the code, and I can't see that it would be possible to get
that error in this context. BASE loads all reporters from the database
into an array, and checks against that to see if reporters are
already known, but if they're not in the array it also checks with
the database, because MySQL's strings are case insensitive whereas
PHP is case sensitive. The other thing that could cause problems then
are trailing spaces, but they're stripped away in the PHP code. So
I guess I'll need to see the message in the error log to make some
sense out of this.

//Carl
--
Carl Troein - ***@thep.lu.se
http://www.thep.lu.se/~carl/
BASE developer - http://base.thep.lu.se/
Paul Rigor
2004-07-06 16:38:09 UTC
Permalink
Hi Carl,

I'm having trouble retrieving my php error log file. It does not exist
where I specified it to be. I've also checked out my apache error logs,
but only access and ssl errors (not related to base) have been logged.
Regarding possible trivial problems: the disk is not full, correct
access privileges have been setup, no corrupt file, and no duplication
of keys.

The original .sql file which I imported contained white spaces, empty
lines and commented lines; however, as the snapshots below show, they
posed no effect.

One thing to note, the minor php changes I've made did include empty
lines and comments within the getColumns() function between the array()
calls. Would that make a difference?

I'll keep you posted on the error logs...

Thanks!
Paul
***@gmail.com (My ucla account fills up too quickly)



PS:

Here's a snapshot of the Reporter table
+------------------------+--------------+------+-----+---------------------+----------------+
| Field | Type | Null | Key |
Default | Extra |
+------------------------+--------------+------+-----+---------------------+----------------+
| id | mediumint(9) | | PRI |
NULL | auto_increment |
| reporterId | varchar(255) | | UNI
| | |
| species | varchar(255) | |
| | |
| clusterId | int(11) | | |
0 | |
| geneName | varchar(255) | | MUL
| | |
| geneSymbol | varchar(255) | |
| | |
| lastUpdate | datetime | | | 0000-00-00
00:00:00 | |
| length | int(11) | YES | |
0 | |
| sequence | text | YES | |
NULL | |
| vector | text | YES | |
NULL | |
| tissue | text | YES | |
NULL | |
| library | text | YES | |
NULL | |
| accession | varchar(255) | YES | |
NULL | |
| nid | varchar(255) | YES | |
NULL | |
| chromosome | varchar(255) | YES | |
NULL | |
| cytoBand | varchar(255) | YES | |
NULL | |
| markers | varchar(255) | YES | |
NULL | |
| antibiotics | varchar(255) | YES | |
NULL | |
| locusLink | int(11) | YES | |
0 | |
| omim | int(11) | YES | |
0 | |
| startPosition | int(11) | YES | |
0 | |
| endPosition | int(11) | YES | |
0 | |
| agilent_FeatureNumber | varchar(255) | |
| | |
| agilent_ug | varchar(255) | |
| | |
| agilent_mgi | varchar(255) | |
| | |
| agilent_ProbeUID | varchar(255) | |
| | |
| agilent_ControlType | tinyint(4) | YES | |
NULL | |
| agilent_SystematicName | varchar(255) | |
| | |
| agilent_Description | varchar(255) | |
| | |
+------------------------+--------------+------+-----+---------------------+----------------+
29 rows in set (0.00 sec)

And here's a snapshot of the RawBioAssayData table


+------------------------+--------------+------+-----+---------+-------+
| Field | Type | Null | Key | Default | Extra |
+------------------------+--------------+------+-----+---------+-------+
| rawBioAssay | mediumint(9) | | PRI | 0 | |
| position | mediumint(9) | | PRI | 0 | |
| element | mediumint(9) | | | 0 | |
| reporter | mediumint(9) | | | 0 | |
| block | smallint(6) | YES | | NULL | |
| numCol | tinyint(4) | YES | | NULL | |
| numRow | tinyint(4) | YES | | NULL | |
| x | float | | | 0 | |
| y | float | | | 0 | |
| dia | float | YES | | NULL | |
| FCh1Median | float | YES | | NULL | |
| FCh1Mean | float | YES | | NULL | |
| FCh1SD | float | YES | | NULL | |
| BCh1Median | float | YES | | NULL | |
| BCh1Mean | float | YES | | NULL | |
| BCh1SD | float | YES | | NULL | |
| percCh1SD1 | tinyint(4) | YES | | NULL | |
| percCh1SD2 | tinyint(4) | YES | | NULL | |
| percCh1Sat | tinyint(4) | YES | | NULL | |
| FCh2Median | float | YES | | NULL | |
| FCh2Mean | float | YES | | NULL | |
| FCh2SD | float | YES | | NULL | |
| BCh2Median | float | YES | | NULL | |
| BCh2Mean | float | YES | | NULL | |
| BCh2SD | float | YES | | NULL | |
| percCh2SD1 | tinyint(4) | YES | | NULL | |
| percCh2SD2 | tinyint(4) | YES | | NULL | |
| percCh2Sat | tinyint(4) | YES | | NULL | |
| ratiosSD | float | YES | | NULL | |
| rgnRatio | float | YES | | NULL | |
| rgnR2 | float | YES | | NULL | |
| FPixels | smallint(6) | YES | | NULL | |
| BPixels | smallint(6) | YES | | NULL | |
| flags | tinyint(4) | YES | | NULL | |
| MValue | float | YES | | NULL | |
| CV | float | YES | | NULL | |
| agilent_LogRatioError | float | YES | | NULL | |
| agilent_PValueLogRatio | float | YES | | NULL | |
| imagene_MetaRow | tinyint(4) | YES | | NULL | |
| imagene_MetaColums | tinyint(4) | YES | | NULL | |
+------------------------+--------------+------+-----+---------+-------+
40 rows in set (0.02 sec)
Post by Carl Troein
Post by RIGOR,PAUL MACARAEG
I'm having a problem adding a raw results file after the "add scan" step.
Error on line 11: Unable to create new reporter '(+)Pro25G-03'
Operation aborted
1) select Hybrization
2) select Scan
3) under Raw data sets, select "upload result file"
4) choose result file format
5) clicking on continue shows the error...
Hmm... it would help to see the error message logged to the PHP (or
Apache) error log, but I think can guess what it is. Unless it's
something as trivial as 'disk full' or 'access denied' (or as nasty
as a corrupted file), it's a duplicate key error of some kind. I've
looked at the code, and I can't see that it would be possible to get
that error in this context. BASE loads all reporters from the database
into an array, and checks against that to see if reporters are
already known, but if they're not in the array it also checks with
the database, because MySQL's strings are case insensitive whereas
PHP is case sensitive. The other thing that could cause problems then
are trailing spaces, but they're stripped away in the PHP code. So
I guess I'll need to see the message in the error log to make some
sense out of this.
//Carl
Carl Troein
2004-07-07 23:08:01 UTC
Permalink
Post by Paul Rigor
I'm having trouble retrieving my php error log file. It does not exist
where I specified it to be. I've also checked out my apache error logs,
but only access and ssl errors (not related to base) have been logged.
Could it be that the file you've specified would be in a directory the
user doesn't have write access to? If so, the easiest solution is
probably to create an empty file there, and give it to the base user.
In general, if PHP can't write to the specified log file, I think it
just gives up silently.
Post by Paul Rigor
One thing to note, the minor php changes I've made did include empty
lines and comments within the getColumns() function between the array()
calls. Would that make a difference?
No, not unless there's a parse error or something similar, but then the
whole thing probably wouldn't work at all.

//Carl
--
Carl Troein - ***@thep.lu.se
http://www.thep.lu.se/~carl/
BASE developer - http://base.thep.lu.se/
N. Immelman
2004-07-08 03:55:06 UTC
Permalink
To quickly find out where php is logging, type from command line "php -i".
This will dump all the configuration options to screen. error_log is the
path to the file php is logging to. Type something like "php -i | grep
error_log" to quickly see what it is set to.

Nicolas
Post by Carl Troein
Post by Paul Rigor
I'm having trouble retrieving my php error log file. It does not exist
where I specified it to be. I've also checked out my apache error logs,
but only access and ssl errors (not related to base) have been logged.
Could it be that the file you've specified would be in a directory the
user doesn't have write access to? If so, the easiest solution is
probably to create an empty file there, and give it to the base user.
In general, if PHP can't write to the specified log file, I think it
just gives up silently.
Post by Paul Rigor
One thing to note, the minor php changes I've made did include empty
lines and comments within the getColumns() function between the array()
calls. Would that make a difference?
No, not unless there's a parse error or something similar, but then the
whole thing probably wouldn't work at all.
//Carl
--
http://www.thep.lu.se/~carl/
BASE developer - http://base.thep.lu.se/
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paul rigor
2004-07-12 13:56:11 UTC
Permalink
okay, so i reproduced the error again and I can finally see an error
log. i'm not sure, but perhaps the old error log was deleted. here is
the error line.

[07-Jul-2004 00:52:37] MySQL query failed: "INSERT INTO Reporter
(`reporterId`,`species`,`clusterId`,`geneName`,`geneSymbol`,`lastUpdate`,`length`,`sequence`,`vector`,`tissue`,`library`,`accession`,`nid`,`chromosome`,`cytoBand`,`markers`,`antibiotics`,`locusLink`,`omim`,`startPosition`,`endPosition`,`agilent_FeatureNumber`,`agilent_ug`,`agilent_mgi`,`agilent_ProbeUID`,`agilent_ControlType`,`agilent_SystematicName`,`agilent_Description`) VALUES ('(+)Pro25G-03', '', '0', '', '', '0000-00-00', NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL)" : Column 'agilent_FeatureNumber' cannot be null

And I found the changes I made in the Reporter table base_mysql.sql
file:
agilent_FeatureNumber varchar(255) NOT NULL default ''...

I've forgotten how to change the properties of a table column. Any
takers while I search through MySql support file?

Thanks,
Paul
Post by N. Immelman
To quickly find out where php is logging, type from command line "php -i".
This will dump all the configuration options to screen. error_log is the
path to the file php is logging to. Type something like "php -i | grep
error_log" to quickly see what it is set to.
Nicolas
Post by Carl Troein
Post by Paul Rigor
I'm having trouble retrieving my php error log file. It does not exist
where I specified it to be. I've also checked out my apache error logs,
but only access and ssl errors (not related to base) have been logged.
Could it be that the file you've specified would be in a directory the
user doesn't have write access to? If so, the easiest solution is
probably to create an empty file there, and give it to the base user.
In general, if PHP can't write to the specified log file, I think it
just gives up silently.
Post by Paul Rigor
One thing to note, the minor php changes I've made did include empty
lines and comments within the getColumns() function between the array()
calls. Would that make a difference?
No, not unless there's a parse error or something similar, but then the
whole thing probably wouldn't work at all.
//Carl
--
http://www.thep.lu.se/~carl/
BASE developer - http://base.thep.lu.se/
-------------------------------------------------------
This SF.Net email sponsored by Black Hat Briefings & Training.
Attend Black Hat Briefings & Training, Las Vegas July 24-29 -
digital self defense, top technical experts, no vendor pitches,
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_________
Go Bruins!
Go Linux!
paul rigor
2004-07-12 16:04:02 UTC
Permalink
Hi,

I have a question regarding upgrading from 1.2.11 to 1.2.12. Are there
significant changes in the sql table definitions? I've setup custom
columns, would I need to modify the dbmigrate php script to include our
custom columns?

Thanks,
Paul
Post by N. Immelman
To quickly find out where php is logging, type from command line "php -i".
This will dump all the configuration options to screen. error_log is the
path to the file php is logging to. Type something like "php -i | grep
error_log" to quickly see what it is set to.
Nicolas
Post by Carl Troein
Post by Paul Rigor
I'm having trouble retrieving my php error log file. It does not exist
where I specified it to be. I've also checked out my apache error logs,
but only access and ssl errors (not related to base) have been logged.
Could it be that the file you've specified would be in a directory the
user doesn't have write access to? If so, the easiest solution is
probably to create an empty file there, and give it to the base user.
In general, if PHP can't write to the specified log file, I think it
just gives up silently.
Post by Paul Rigor
One thing to note, the minor php changes I've made did include empty
lines and comments within the getColumns() function between the array()
calls. Would that make a difference?
No, not unless there's a parse error or something similar, but then the
whole thing probably wouldn't work at all.
//Carl
--
http://www.thep.lu.se/~carl/
BASE developer - http://base.thep.lu.se/
-------------------------------------------------------
This SF.Net email sponsored by Black Hat Briefings & Training.
Attend Black Hat Briefings & Training, Las Vegas July 24-29 -
digital self defense, top technical experts, no vendor pitches,
unmatched networking opportunities. Visit www.blackhat.com
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unsubscribe: send a mail with subject "unsubscribe" to
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digital self defense, top technical experts, no vendor pitches,
unmatched networking opportunities. Visit www.blackhat.com
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basedb-users-***@lists.sourceforge.net


_________
Go Bruins!
Go Linux!

paul rigor
2004-07-12 15:19:04 UTC
Permalink
Our problem has been fixed! Thanks for everyone's help!

While I was modifying the custom column definitions, I also spotted a
couple of spelling errors. Well, so much for being careful.

Thanks again!
Paul
Post by Carl Troein
Post by Paul Rigor
I'm having trouble retrieving my php error log file. It does not exist
where I specified it to be. I've also checked out my apache error logs,
but only access and ssl errors (not related to base) have been logged.
Could it be that the file you've specified would be in a directory the
user doesn't have write access to? If so, the easiest solution is
probably to create an empty file there, and give it to the base user.
In general, if PHP can't write to the specified log file, I think it
just gives up silently.
Post by Paul Rigor
One thing to note, the minor php changes I've made did include empty
lines and comments within the getColumns() function between the array()
calls. Would that make a difference?
No, not unless there's a parse error or something similar, but then the
whole thing probably wouldn't work at all.
//Carl
_________
Go Bruins!
Go Linux!
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