Re: [Gmod-gbrowse] Uploaded tracks

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Re: [Gmod-gbrowse] Uploaded tracks

Jayaraman, Pushkala

Hey guys..

Has anyone come across this problem..?

I haven’t been able to resolve this for a few days now..

To add to my debugging attempts.. I even checked if SQLite was installed correctly.. Ii wrote my own perl script that created a new database using SQLite.. I am also able to run SQLite in the cmd line..

There is no username and password set..

 

But I still see the error logs showing these messages..

mod_fcgid: stderr: DBD::SQLite::st execute failed: called with 2 bind variables when 3 are needed

im guessing it needs more parameters.. but isn’t getting any..

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala
Sent: Wednesday, August 17, 2011 11:23 AM
To: Jayaraman, Pushkala; Lincoln Stein; Frédéric Sapet
Cc: gmod-gbrowse
Subject: RE: [Gmod-gbrowse] Uploaded tracks

 

In the error Logs I now see:

mod_fcgid: stderr: DBD::SQLite::st execute failed: called with 2 bind variables when 3 are needed

 

any clues as to what I need to set right?

 

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Jayaraman, Pushkala [mailto:[hidden email]]
Sent: Wednesday, August 17, 2011 11:06 AM
To: Lincoln Stein; Frédéric Sapet
Cc: gmod-gbrowse
Subject: Re: [Gmod-gbrowse] Uploaded tracks

 

Hello,

 

I read this thread about configuring DBI::SQLite..

I am running into a slightly different problem..

 

I am not able to view my uploaded track.. although the upload happens normally and the database gets created ( or so I presume) in the file system as I can see the following folders for each Gff3 file

 

total 96

-rw-r--r-- 1 rgdpub rgdpub   563 Aug 17 10:50 upload_80583.conf

-rw-r--r-- 1 rgdpub rgdpub 81920 Aug 17 10:50 index.SQLite

drwxr-xr-x 2 rgdpub rgdpub  4096 Aug 17 10:50 SOURCES

-rw-r--r-- 1 rgdpub rgdpub    20 Aug 17 10:50 STATUS

 

But the Gbrowse user is ‘rgdselect’ and not rgdoub..

Would that be a problem…?

 

There seem to be no errors in the apache logs..

What am I doing wrong..?

 

 

Herewith is my Gbrowse.conf file attached:

 

##############some stuff###############

 

# These paths are relative to the config base

plugin_path    = plugins

language_path  = languages

templates_path = templates

moby_path      = MobyServices

 

# session settings

session lock type = default

 

# If no session driver is set, then GBrowse will pick one for you.

# It will use db_file for the driver and storable for the serializer

# if available; otherwise falling back to the file driver and default serializer.

 

# Override driver guessing by setting these options

# The safest, but slowest session driver...

#session driver    = driver:file;serializer:default

#session args      = Directory /rgd/gbrowse2/tmp/sessions

 

# to use the berkeley DB driver comment out the previous

# line and uncomment these two

#session driver = driver:db_file;serializer:default

#session args   = FileName /rgd/gbrowse2/tmp/sessions.db

 

# DBI backend to use for uploaded userdata.

# The SQLite option is the easiest to use and the best tested.

# if this option is commented out, then GBrowse will

# try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'

# backend.

 

# For the DBI::mysql adaptor to work, you must give the web user

# permission to create databases named userdata_% using the following

# mysql command:

#    mysql> grant all privileges on `userdata\_%`.* to 'www-data'@localhost identified by 'foobar';

# Note the backquotes around the database name, and do be sure to replace "foobar" with

# a more secure password!

 

# for SQLite

upload_db_adaptor = DBI::SQLite

 

# for Berkeleydb

#upload_db_adaptor = berkeleydb

 

# for mysql

#userdb_adaptor = DBI::mysql

#userdb_host    = irvine.hmgc.mcw.edu

#userdb_user    = rgdselect

#userdb_pass    =

 

 

 

# Debug settings

debug                  = 1

debug_external         = 1

debug_plugins          = 1

 

# Performance settings

renderfarm             = 1

slave_timeout          = 45

global_timeout         = 60

search_timeout         = 15

max_render_processes   = 4   # try double number of CPU/cores

 

# Clean up settings (used by the gbrowse_clean script)

# expire unused sessions after a day

expire session  = 1d 

# expire cached data if unmodified for >1 hours

expire cache    = 1h 

# expire uploaded data if unused for >1 day

expire uploads  = 1d 

 

# Appearance settings

truecolor     =  1   # better appearance at the expense of larger image files

 

# The #include line following this one defines a transparent theme.

# Replace "transparent_colors" with "solid_gray_colors"

# or "warm_colors" for different themes.

 

# #include "themes/warm_colors"

#include "themes/transparent_colors"

# #include "themes/solid_gray_colors"

 

balloon tips        = 1

titles are balloons = 1

plugins             = FastaDumper RestrictionAnnotator SequenceDumper TrackDumper

overview grid       = 1

region grid         = 1

detail grid         = 1

image widths        = 450 640 720 800 1024

default width       = 770

pad_left            = 75

pad_right           = 85

too many landmarks  = 100

 

###some more stuff#####

 

####### User Account Registration Database ######

# If "user accounts" is true, then we will try to use

# a user registration database

user accounts          = 0

 

# Path to the database -- you will need to create this database and grant all

# privileges on it to the indicated user.

user_account_db        = /rgd/gbrowse2/databases/users.sqlite

 

# What email gateway to use for outgoing registration confirmation messages.

# The full format is

#      <smtp.server.com>:<port>:<encryption>:<username>:<password>

# Only the first field, the server name, is required.

#    The port is assumed to be 25 unless ssl encryption is specified, in

#               which case it defaults to 465.

#    protocol is either "plain" or "ssl", "plain" assumed.

#    username and password may be required by the gateway for authentication

smtp_gateway           = smtp.gmail.com:465:ssl:authorized_user:authorized_password

 

# These values are used in the login confirmation message sent during

# user registration. You may customize

application_name       = GBrowse

application_name_long  = The Generic Genome Browser

email_address          = [hidden email]

 

# name of the "superuser" who can add public tracks

admin_account          = admin

admin_dbs              = /rgd/gbrowse2/databases/admin_uploads

 

#######################more stuff##################

 

 

Thanks,

Pushkala Jayaraman

Programmer/Analyst

Rat Genome Database

Human and Molecular Genetics Center

Medical College of Wisconsin

Email: [hidden email]

Work: 414-955-2229

www.rgd.mcw.edu

 

From: Lincoln Stein [mailto:[hidden email]]
Sent: Thursday, September 02, 2010 11:38 AM
To: Frédéric Sapet
Cc: gmod-gbrowse
Subject: Re: [Gmod-gbrowse] Uploaded tracks

 

Thank you for your brilliant detective work. This will help me track down and fix the problem.

 

Lincoln

2010/9/2 Frédéric Sapet <[hidden email]>

Hello

It works if I set render_farm = 0 in my config file.

I try with  :
renderfarm             = 1
#userdb_adaptor = DBI::SQLite
and I see then  "No userdb_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite." but also  "Can't call method "Flush" without a package or object reference" and no user track is shown

with
renderfarm             = 0
#userdb_adaptor = DBI::SQLite
I see then  "No userdb_adaptor option set in GBrowse.conf. Will try to use DBI::SQLite." but in this case my user track is displayed

with
renderfarm             = 0
userdb_adaptor = DBI::SQLite
there is no more warning in apache log and I see my track

It works also with userdb_adaptor = memory and renderfarm             = 0

Fred

Le 31 août 2010 19:23, Frédéric Sapet <[hidden email]> a écrit :

 

Hello Prem

I will try what you say.

Thanks

Fred

Le 31 août 2010 18:58, Prem Anand <[hidden email]> a écrit :

 

Hi Fred

We too had issues with upload and later we switched to SQLite adaptor
it worked. Try to use this in your GBrowse.conf, it may work

#user accounts          = 0
#user_account_db

userdb_adaptor = DBI::SQLite

Thanks
Prem


2010/8/31 Lincoln Stein <[hidden email]>:

> During the upload, do you see the upload progress (spinning wheel and a


> message saying "uploading" and "processing") or do you get the error message
> right away after hitting the "Upload" button?
> Lincoln
>
> 2010/8/31 Frédéric Sapet <[hidden email]>
>>
>> My userdbadaptor is commented, and if the GBrowse.conf sample given in
>> 2.13, I can read :
>> # DBI backend to use for uploaded userdata.
>> # The SQLite option is better tested
>> # if this option is commented out, then GBrowse will
>> # try 'DBI::SQLite', 'berkeleydb', 'DBI::mysql' and finally the 'memory'
>> # backend.
>>
>> So it's why I thought that memory was the default adaptor.
>>
>> By the way, even with userdbadaptor commented  I do not see any "No
>> upload_db_adaptor option set in GBrowse.conf. Will try to use memory."
>> message in my log.
>>
>> And I have the same error Can't call method "Flush" with userdb_adaptor =
>> memory in my GBrowse.conf (my data source config file is clear of this kind
>> of option, there is only tracks definition out there)
>>
>> Fred
>>
>> Le 31 août 2010 16:58, Lincoln Stein <[hidden email]> a écrit :
>>>
>>> I tried the memory adaptor myself just now and it seems to be working in
>>> my hands. If userdb_adaptor is commented completely in both the data source
>>> and the GBrowse.conf file, then you ought to be seeing a message like this
>>> one in the error log:
>>>
>>> No upload_db_adaptor option set in GBrowse.conf. Will try to use memory.
>>> at /home/lstein/projects/GBrowse/lib/Bio/Graphics/Browser2/DataLoader.pm
>>> line 357.
>>>
>>> Do you see it, and if so, which backend is it indicating that it is
>>> trying?
>>> Lincoln
>>> 2010/8/31 Frédéric Sapet <[hidden email]>
>>>>
>>>> Hi,
>>>>
>>>> I'm running GGB under Mod_perl but I have also the error when running
>>>> usual cgi.
>>>>
>>>> My userdb_adaptor is commented out so memory seems to be the backend.
>>>>
>>>> Thanks
>>>>
>>>> Fred
>>>>
>>>> Le 31 août 2010 16:23, Lincoln Stein <[hidden email]> a écrit :
>>>>>
>>>>> What are your settings for userdb_adaptor, and are you running in a
>>>>> regular CGI environment, or using FastCGI?
>>>>> You could try gbrowse version 2.14, where there was a lot of work done
>>>>> on upload functionality, but I don't immediately understand what is
>>>>> generating the Flush error.
>>>>>
>>>>> Lincoln
>>>>>
>>>>> 2010/8/31 Frédéric Sapet <[hidden email]>
>>>>>>
>>>>>> Hi,
>>>>>> I am configurating Gbrowse 2.13, most of features work properly but I
>>>>>> am encoutering a bug when I try to upload tracks (using the upload and share
>>>>>> Tracks tab) :
>>>>>> "Can't call method "Flush" without a package or object reference. no
>>>>>> details". printed directly in the browser, my apache error log file is
>>>>>> empty...
>>>>>>
>>>>>> Here is the text I have uploaded (Chr1 is a valid reference) :
>>>>>> EST    yk260e10.5    Chr1:1..15
>>>>>> EST    yk672a12.5    Chr1:50..200
>>>>>> EST    yk595e6.5    Chr1:300..456
>>>>>>
>>>>>> and here the conf generated :
>>>>>>
>>>>>> [EST_1]
>>>>>> database = database_0 # do not change this!
>>>>>> feature   = EST
>>>>>> glyph     = segments
>>>>>> bgcolor   = green
>>>>>> fgcolor   = black
>>>>>> label     = 1
>>>>>> stranded  = 1
>>>>>> connector = solid
>>>>>> balloon hover = $description
>>>>>> category    = My Tracks:Uploaded Tracks:upload_582
>>>>>> key         = EST
>>>>>>
>>>>>> When I go back to the browser, the track is loaded, but no feature
>>>>>> appear !
>>>>>>
>>>>>> I checked my GBrowse.conf file and I am sure that user account is not
>>>>>> allowed :
>>>>>> user accounts     = 0
>>>>>> user_account_db = memory
>>>>>>
>>>>>> Regards,
>>>>>> Frederic
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> This SF.net Dev2Dev email is sponsored by:
>>>>>>
>>>>>> Show off your parallel programming skills.
>>>>>> Enter the Intel(R) Threading Challenge 2010.
>>>>>> http://p.sf.net/sfu/intel-thread-sfd
>>>>>> _______________________________________________
>>>>>> Gmod-gbrowse mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Lincoln D. Stein
>>>>> Director, Informatics and Biocomputing Platform
>>>>> Ontario Institute for Cancer Research
>>>>> 101 College St., Suite 800
>>>>> Toronto, ON, Canada M5G0A3
>>>>> 416 673-8514
>>>>> Assistant: Renata Musa <[hidden email]>
>>>>
>>>
>>>
>>>
>>> --
>>> Lincoln D. Stein
>>> Director, Informatics and Biocomputing Platform
>>> Ontario Institute for Cancer Research
>>> 101 College St., Suite 800
>>> Toronto, ON, Canada M5G0A3
>>> 416 673-8514
>>> Assistant: Renata Musa <[hidden email]>
>>
>
>
>
> --
> Lincoln D. Stein
> Director, Informatics and Biocomputing Platform
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Renata Musa <[hidden email]>
>
> ------------------------------------------------------------------------------
> This SF.net Dev2Dev email is sponsored by:
>
> Show off your parallel programming skills.
> Enter the Intel(R) Threading Challenge 2010.
> http://p.sf.net/sfu/intel-thread-sfd
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

 

 



--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>


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