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:
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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
