-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 >>>> >>>> >>>> >>>> >>>> >>>> >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFtzOY4C5LeMEKA/QRApiCAKCWFeT21fTl+1S4NuNMLCu07JqVywCgiFQ2 kgc3fxzvnxQ9OUgkjWfBLNM= =ouGx -----END PGP SIGNATURE-----
