Thanks for your help - it seems all it needed was the --clean switch.
Thanks again,
Jennifer
Richard Holland wrote:
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Now I'm confused. :)
The error message you get suggests that the system fails to load the
registry object. This is the code that is throwing the error:
# This assigns undef to mart_registry if there is no system
# registry object.
my $mart_registry = $self->get_mart_registry();
# This line fails if mart_registry is undef.
my $hash = $mart_registry->settingsParams();
As you can see, it is somehow failing to pick up the registry object.
When you configured, did you use the --clean switch? If not, try using that.
Also, answer 'N' to 'keep existing server settings' and re-enter them.
This will make sure it hasn't cached away some dodgy registry object
somewhere.
If it still fails, double-check that you have write permissions to the
conf/ folder and all of its sub-folders, and that the Apache user
account also has both read- and write-access to the same location (do a
ps -ef to find out what user account Apache is running as).
cheers,
Richard
Jennifer Siepen wrote:
Sorry about that, I got confused...this is the registry XML
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<virtualSchema name="default" visible="1" default="1">
<MartDBLocation
name = "registerMart"
displayName = "registerMart"
host = "10.127.1.12"
port = "3306"
database = "registerMart"
schema = "registerMart"
user = "ispider_web"
password = "****"
visible = "1"
default = ""
databaseType = "mysql"
includeMarts = ""
/>
</virtualSchema>
</MartRegistry>
Jennifer
Richard Holland wrote:
Hello again.
That's not registry XML. That's the XML that MartBuilder uses to store
dataset definitions when you use the File->Save menu option, so that you
can continue working with them later if you need to. If this is the file
that you gave the bin/configure.pl script using the -r switch then I'm
surprised it worked at all - the script simply doesn't work if you don't
give it a valid registry XML file.
To get from MartBuilder to a working MartView you need to do this:
1) Define your mart in MartBuilder (looks like you've already done this)
2) Use MartBuilder to generate SQL that will create the mart out of your
source data. Run that SQL.
3) Connect to the created mart using MartEditor and configure the
attributes and filters you want (the Naive option will do this for you
with sensible defaults)
4) Export the config from MartEditor so that it is saved in your mart
5) Create a registry XML file that describes how to find your newly
configured mart
6) Run bin/configure.pl using the registry XML
7) Start up MartView
cheers,
Richard
Jennifer Siepen wrote:
Hi,
Have you configured BioMart using the bin/configure.pl script? If not,
you need to do that first.
Yes, I did this.
If you have done this already, then please could you put the
contents of
the registry XML into an email (not an attachment as this list does not
accept them). We can then take a look at it.
Here is the xml.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE mart PUBLIC "-//EBI//DTD MartBuilder 0.5//EN"
"http://www.biomart.org/DTD/MartBuilder-0.5.dtd";>
<mart>
<jdbcSchema driverClassName="com.mysql.jdbc.Driver"
url="jdbc:mysql://10.127.1.12:3306/ispiderRegistry"
schemaName="ispiderRegistry" username="ispider_web" password="*******"
name="ispiderRegistry" keyguessing="true">
<table id="1" name="Input" originalName="Input">
<column id="2" name="dataType"
originalName="dataType"/>
<column id="3" name="description"
originalName="description"/>
<column id="4" name="input_id"
originalName="input_id"/>
<column id="5" name="ispiderType"
originalName="ispiderType"/>
<column id="6" name="localName"
originalName="localName"/>
<column id="7" name="operation_id"
originalName="operation_id"/>
<column id="8" name="optional"
originalName="optional"/>
<primaryKey id="9" columnIds="4"
status="INFERRED" alt="PK_ispiderRegistry:Input[input_id]"/>
</table>
<table id="10" name="Output" originalName="Output">
<column id="11" name="dataType"
originalName="dataType"/>
<column id="12" name="description"
originalName="description"/>
<column id="13" name="ispiderType"
originalName="ispiderType"/>
<column id="14" name="localName"
originalName="localName"/>
<column id="15" name="operation_id"
originalName="operation_id"/>
<column id="16" name="output_id"
originalName="output_id"/>
<primaryKey id="17" columnIds="16"
status="INFERRED" alt="PK_ispiderRegistry:Output[output_id]"/>
</table>
<table id="18" name="Resource" originalName="Resource">
<column id="19" name="endpoint"
originalName="endpoint"/>
<column id="20" name="resourceType"
originalName="resourceType"/>
<column id="21" name="resource_id"
originalName="resource_id"/>
<primaryKey id="22" columnIds="21"
status="INFERRED" alt="PK_ispiderRegistry:Resource[resource_id]"/>
</table>
<table id="23" name="Service" originalName="Service">
<column id="24" name="description"
originalName="description"/>
<column id="25" name="endpoint"
originalName="endpoint"/>
<column id="26" name="limitedAccess"
originalName="limitedAccess"/>
<column id="27" name="name" originalName="name"/>
<column id="28" name="provider"
originalName="provider"/>
<column id="29" name="serviceType"
originalName="serviceType"/>
<primaryKey id="30" columnIds="25"
status="INFERRED" alt="PK_ispiderRegistry:Service[endpoint]"/>
</table>
<table id="31" name="ServiceOperation"
originalName="ServiceOperation">
<column id="32" name="description"
originalName="description"/>
<column id="33" name="endpoint"
originalName="endpoint"/>
<column id="34" name="name" originalName="name"/>
<column id="35" name="operation_id"
originalName="operation_id"/>
<column id="36" name="wrapper"
originalName="wrapper"/>
<primaryKey id="37" columnIds="35"
status="INFERRED"
alt="PK_ispiderRegistry:ServiceOperation[operation_id]"/>
</table>
<table id="38" name="news" originalName="news">
<column id="39" name="date" originalName="date"/>
<column id="40" name="id" originalName="id"/>
<column id="41" name="text" originalName="text"/>
<primaryKey id="42" columnIds="40"
status="INFERRED" alt="PK_ispiderRegistry:news[id]"/>
</table>
<table id="43" name="register" originalName="register">
<column id="44" name="display_type"
originalName="display_type"/>
<column id="45" name="howtorun"
originalName="howtorun"/>
<column id="46" name="id" originalName="id"/>
<column id="47" name="input"
originalName="input"/>
<column id="48" name="limited"
originalName="limited"/>
<column id="49" name="output"
originalName="output"/>
<column id="50" name="service"
originalName="service"/>
<primaryKey id="51" columnIds="46"
status="INFERRED" alt="PK_ispiderRegistry:register[id]"/>
</table>
<table id="52" name="register_output"
originalName="register_output">
<column id="53" name="id" originalName="id"/>
<column id="54" name="output_type"
originalName="output_type"/>
<column id="55" name="register_id"
originalName="register_id"/>
<foreignKey id="56" columnIds="55"
status="INFERRED"
alt="FK_ispiderRegistry:register_output[register_id]"/>
</table>
<table id="57" name="webPage" originalName="webPage">
<column id="58" name="attSeperation"
originalName="attSeperation"/>
<column id="59" name="operation_id"
originalName="operation_id"/>
<column id="60" name="resource_id"
originalName="resource_id"/>
<column id="61" name="url" originalName="url"/>
<column id="62" name="valueSeperation"
originalName="valueSeperation"/>
<primaryKey id="63" columnIds="59"
status="INFERRED" alt="PK_ispiderRegistry:webPage[operation_id]"/>
</table>
<table id="64" name="webService" originalName="webService">
<column id="65" name="description"
originalName="description"/>
<column id="66" name="limitedAccess"
originalName="limitedAccess"/>
<column id="67" name="name" originalName="name"/>
<column id="68" name="provider"
originalName="provider"/>
<column id="69" name="resource_id"
originalName="resource_id"/>
<column id="70" name="service_id"
originalName="service_id"/>
<primaryKey id="71" columnIds="70"
status="INFERRED" alt="PK_ispiderRegistry:webService[service_id]"/
</table>
<relation id="72" cardinality="M" firstKeyId="51"
secondKeyId="56" status="INFERRED" alt="PK_ispiderRegistry:
register[id]:FK_ispiderRegistry:register_output[register_id]"/>
</jdbcSchema>
<dataset name="register" centralTableId="43"
alt="ispiderRegistry:register" optimiser="NONE" invisible="false">
<table id="73" name="register" originalName="register"
type="MAIN" underlyingTableId="43" underlyingRelationI
ds="" underlyingKeyIds="">
<column id="74" name="display_type"
originalName="display_type" underlyingRelationId="null" dependenc
y="false" masked="false" alt="null" type="wrapped" wrappedColumnId="44"
wrappedColumnAlt="ispiderRegistry:register:display_ty
pe" partitionType="null"/>
<column id="75" name="howtorun"
originalName="howtorun" underlyingRelationId="null" dependency="false
" masked="false" alt="null" type="wrapped" wrappedColumnId="45"
wrappedColumnAlt="ispiderRegistry:register:howtorun" partitio
nType="null"/>
<column id="76" name="id_key" originalName="id"
underlyingRelationId="null" dependency="true" masked=
"false" alt="null" type="wrapped" wrappedColumnId="46"
wrappedColumnAlt="ispiderRegistry:register:id" partitionType="null"/>
<column id="77" name="input" originalName="input"
underlyingRelationId="null" dependency="false" mask
ed="false" alt="null" type="wrapped" wrappedColumnId="47"
wrappedColumnAlt="ispiderRegistry:register:input" partitionType="nu
ll"/>
<column id="78" name="limited"
originalName="limited" underlyingRelationId="null" dependency="false"
masked="false" alt="null" type="wrapped" wrappedColumnId="48"
wrappedColumnAlt="ispiderRegistry:register:limited" partitionTy
pe="null"/>
<column id="79" name="output"
originalName="output" underlyingRelationId="null" dependency="false" ma
sked="false" alt="null" type="wrapped" wrappedColumnId="49"
wrappedColumnAlt="ispiderRegistry:register:output" partitionType=
"null"/>
<column id="80" name="service"
originalName="service" underlyingRelationId="null" dependency="false"
masked="false" alt="null" type="wrapped" wrappedColumnId="50"
wrappedColumnAlt="ispiderRegistry:register:service" partitionTy
pe="null"/>
<primaryKey id="81" columnIds="76"
status="INFERRED" alt="PK_register:register[id_key]"/>
</table> <table id="82"
name="register_output" originalName="register_output" type="DIMENSION"
underlyingTableId="52"
underlyingRelationIds="72" underlyingKeyIds="51" sourceRelationId="72">
<column id="83" name="id" originalName="id"
underlyingRelationId="72" dependency="false" masked="fals
e"
alt="PK_ispiderRegistry:register[id]:FK_ispiderRegistry:register_output[register_id]"
type="wrapped" wrappedColumnId="53"
wrappedColumnAlt="ispiderRegistry:register_output:id"
partitionType="null"/>
<column id="84" name="id_key" originalName="id"
underlyingRelationId="null" dependency="false" masked="false" alt="null"
type="inherited" inheritedColumnId="76"
inheritedColumnAlt="register:register:id_key" partitionType="null"/>
<column id="85" name="output_type"
originalName="output_type" underlyingRelationId="72" dependency="false"
masked="false"
alt="PK_ispiderRegistry:register[id]:FK_ispiderRegistry:register_output[register_id]"
type="wrapped" wrappedColumnId="54"
wrappedColumnAlt="ispiderRegistry:register_output:output_type"
partitionType="null"/>
<foreignKey id="86" columnIds="84"
status="INFERRED" alt="FK_register:register_output[id_key]"/>
</table>
<relation id="87" cardinality="M" firstKeyId="81"
secondKeyId="86" status="INFERRED"
alt="PK_register:register[id_key]:FK_register:register_output[id_key]"/>
</dataset>
</mart>
Thanks,
Jennifer
Richard Holland wrote:
This is related to the contents of your registry.
Have you configured BioMart using the bin/configure.pl script? If not,
you need to do that first.
If you have done this already, then please could you put the contents of
the registry XML into an email (not an attachment as this list does not
accept them). We can then take a look at it.
cheers,
Richard
Jennifer Siepen wrote:
Hi,
I am having some problems getting martview to work. I have tried
numerous things and checked the permissions on the files within
/conf,
all of which seem to be ok. I have also tried deleting and doing a
fresh download a few times still with no luck.
This is the error I get, it remains even when I click 'start new
session'.
ERROR: caught BioMart::Exception: non-BioMart die(): Can't call
method
"settingsParams" on an undefined value at
/fs/ispider/www/localhost/cgi-bin/pepseeker2/biomart-perl/lib/BioMart/Web.pm
line 116.
If you repeatedly get directed to this error page, there may be a
problem with your current session parameters. To clear your
session and
start with a clean slate, please click the button below.
Stacktrace:
Exception::Class::Base::new
/fs/ispider/www/localhost/cgi-bin/pepseeker2/biomart-perl/cgi-bin/martview:78
Any help would be much appreciated.
Thank you,
Jennifer
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--
Dr. Jennifer Siepen
Faculty of Life Sciences,
University of Manchester,
Smith Building, Oxford Rd,
Manchester, M13 9PT, UK.
Tel: +44 (0)161 2751680
