-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> > > > > >> -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFFtzgW4C5LeMEKA/QRAp+DAJ9iDSYNA7f29vsyxonJTzji8KvmoQCdGPgz jkPSLN4l7d03LaRsgw6NhIE= =Xfop -----END PGP SIGNATURE-----
