[BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5)

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[BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5)

Jorge Zamora-2
Hello,

We have realized of some differences from our local ICGC mart with
respect to the web menu for other countries. We're using the icgc xml
that came with rc5. Specifically we're missing the following fields in
the web site:

- 'Gene type' and 'Mutation type' in ANALYSIS within both the 'Affected
Genes' and 'Affected Pathways' sections.
- 'Gene type' in DATABASE SEARCH within 'Genes' section.

is there any extra configuration needed in martconfigurator to display
this information?

Thanks
Jorge

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[BioMart Users] strange message after java error

Alexis
Hello

I was reading some of my logs and found something strange :

         at
org.biomart.configurator.controller.MartController.constructMartRegsitry(MartController.java:1672)

it's a mislocation of letters at Regsitry

A definition of a Regsitry can be found at

./src/org/biomart/configurator/controller/MartController.java:  private
void constructMartRegsitry(MartRegistry registry, Element registryElement) {

Is it controlled?? do you have a biohazard container around it :) ???

    thanks

Alexis

....biomart-path.../logs> head stdouterr.2011_04_05.log
2011-04-05 10:01:24,389 INFO  [main:Log.java:153]: Loading resources
from org/biomart/configurator/resources/messages
2011-04-05 10:01:24,401 INFO  [main:Log.java:153]: Done loading resources
2011-04-05 10:01:31,013 ERROR [main:Log.java:197]: null column
org.biomart.common.exceptions.AssociationException: The two keys cant be
related as they dont share the same number of columns.
         at
org.biomart.objects.objects.Relation.setStatus(Relation.java:262)
         at
org.biomart.objects.objects.Relation.synchronizedFromXML(Relation.java:552)
         at
org.biomart.objects.objects.Mart.synchronizedFromXML(Mart.java:694)
         at
org.biomart.objects.objects.MartRegistry.synchronizedFromXML(MartRegistry.java:228)
         at
org.biomart.configurator.controller.MartController.constructMartRegsitry(MartController.java:1672)
         at
org.biomart.configurator.controller.MartController.requestCreateRegistryFromXML(MartController.java:1649)


WARNING / LEGAL TEXT: This message is intended only for the use of the
individual or entity to which it is addressed and may contain
information which is privileged, confidential, proprietary, or exempt
from disclosure under applicable law. If you are not the intended
recipient or the person responsible for delivering the message to the
intended recipient, you are strictly prohibited from disclosing,
distributing, copying, or in any way using this message. If you have
received this communication in error, please notify the sender and
destroy and delete any copies you may have received.

http://www.bsc.es/disclaimer.htm
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Re: [BioMart Users] strange message after java error

Yong Liang
Hi Alexis,

Don't worry about it. It is safe to ignore this error message. :).  Sorry
for the confusing log message, we will handle it in a better way later.

Yong


On 11-04-06 9:53 AM, "Alexis" <[hidden email]> wrote:

> Hello
>
> I was reading some of my logs and found something strange :
>
>          at
> org.biomart.configurator.controller.MartController.constructMartRegsitry(MartC
> ontroller.java:1672)
>
> it's a mislocation of letters at Regsitry
>
> A definition of a Regsitry can be found at
>
> ./src/org/biomart/configurator/controller/MartController.java:  private
> void constructMartRegsitry(MartRegistry registry, Element registryElement) {
>
> Is it controlled?? do you have a biohazard container around it :) ???
>
>     thanks
>
> Alexis
>
> ....biomart-path.../logs> head stdouterr.2011_04_05.log
> 2011-04-05 10:01:24,389 INFO  [main:Log.java:153]: Loading resources
> from org/biomart/configurator/resources/messages
> 2011-04-05 10:01:24,401 INFO  [main:Log.java:153]: Done loading resources
> 2011-04-05 10:01:31,013 ERROR [main:Log.java:197]: null column
> org.biomart.common.exceptions.AssociationException: The two keys cant be
> related as they dont share the same number of columns.
>          at
> org.biomart.objects.objects.Relation.setStatus(Relation.java:262)
>          at
> org.biomart.objects.objects.Relation.synchronizedFromXML(Relation.java:552)
>          at
> org.biomart.objects.objects.Mart.synchronizedFromXML(Mart.java:694)
>          at
> org.biomart.objects.objects.MartRegistry.synchronizedFromXML(MartRegistry.java
> :228)
>          at
> org.biomart.configurator.controller.MartController.constructMartRegsitry(MartC
> ontroller.java:1672)
>          at
> org.biomart.configurator.controller.MartController.requestCreateRegistryFromXM
> L(MartController.java:1649)
>
>
> WARNING / LEGAL TEXT: This message is intended only for the use of the
> individual or entity to which it is addressed and may contain
> information which is privileged, confidential, proprietary, or exempt
> from disclosure under applicable law. If you are not the intended
> recipient or the person responsible for delivering the message to the
> intended recipient, you are strictly prohibited from disclosing,
> distributing, copying, or in any way using this message. If you have
> received this communication in error, please notify the sender and
> destroy and delete any copies you may have received.
>
> http://www.bsc.es/disclaimer.htm
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users



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Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5)

Junjun Zhang
In reply to this post by Jorge Zamora-2
Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5) Hi Jorge,

We were trying to reproduce the problems at our side, but couldn’t get what you experienced. The problem might be caused by running incorrect UPDATE. We are developing a command line UPDATE tool for ICGC members, the tool will automate the operation as much as possible to minimize the chance of such type of errors.

Best,
Junjun


On 11-04-05 5:35 AM, "Jorge Zamora" <jazamora@...> wrote:

Hello,

We have realized of some differences from our local ICGC mart with
respect to the web menu for other countries. We're using the icgc xml
that came with rc5. Specifically we're missing the following fields in
the web site:

- 'Gene type' and 'Mutation type' in ANALYSIS within both the 'Affected
Genes' and 'Affected Pathways' sections.
- 'Gene type' in DATABASE SEARCH within 'Genes' section.

is there any extra configuration needed in martconfigurator to display
this information?

Thanks
Jorge

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

_______________________________________________
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Users@...
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Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5)

Jorge Zamora-2
Hi Junjun,

I've fully installed rc5, reconfigured icgc3.xml and It makes no
difference. It seems to me that the icgc3.xml that comes with the
installation has a different configuration compared to the one displayed
at http://dcc.icgc.org/, at least in the filter section of the
'ANYLISIS' and 'DATABASE SEARCH'.

Also, is there any graphic library that we should additionally install
to visualize the histograms/bars when resquesting KEGG pathways? I just
ask this since we have set up our local ICGC mart in two independent
machines. In both cases we tell there are differences in the
configuration compared to http://dcc.icgc.org/. However one only machine
displays KEGG pathways. That's why we're where suspecting there're
missing graphic libraries.

Thanks,
Jorge



Junjun Zhang wrote:

> Hi Jorge,
>
> We were trying to reproduce the problems at our side, but couldn’t get
> what you experienced. The problem might be caused by running incorrect
> UPDATE. We are developing a command line UPDATE tool for ICGC members,
> the tool will automate the operation as much as possible to minimize
> the chance of such type of errors.
>
> Best,
> Junjun
>
>
> On 11-04-05 5:35 AM, "Jorge Zamora" <[hidden email]> wrote:
>
>     Hello,
>
>     We have realized of some differences from our local ICGC mart with
>     respect to the web menu for other countries. We're using the icgc xml
>     that came with rc5. Specifically we're missing the following fields in
>     the web site:
>
>     - 'Gene type' and 'Mutation type' in ANALYSIS within both the
>     'Affected
>     Genes' and 'Affected Pathways' sections.
>     - 'Gene type' in DATABASE SEARCH within 'Genes' section.
>
>     is there any extra configuration needed in martconfigurator to display
>     this information?
>
>     Thanks
>     Jorge
>
>     **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso
>     los ficheros adjuntos, pueden contener información protegida para
>     el uso exclusivo de su destinatario. Se prohíbe la distribución,
>     reproducción o cualquier otro tipo de transmisión por parte de
>     otra persona que no sea el destinatario. Si usted recibe por error
>     este correo, se ruega comunicarlo al remitente y borrar el mensaje
>     recibido.
>     **CONFIDENTIALITY NOTICE** This email communication and any
>     attachments may contain confidential and privileged information
>     for the sole use of the designated recipient named above.
>     Distribution, reproduction or any other use of this transmission
>     by any party other than the intended recipient is prohibited. If
>     you are not the intended recipient please contact the sender and
>     delete all copies.
>
>     _______________________________________________
>     Users mailing list
>     [hidden email]
>     https://lists.biomart.org/mailman/listinfo/users
>


**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Re: [BioMart Users] strange message after java error

Alexis
In reply to this post by Yong Liang



Thanks Yong :)

the matter is I thought it could be related to other issues I'm trying
to solve at my mart.

    regards

On 04/06/2011 04:26 PM, Yong Liang wrote:

> Hi Alexis,
>
> Don't worry about it. It is safe to ignore this error message. :).  Sorry
> for the confusing log message, we will handle it in a better way later.
>
> Yong
>
>
> On 11-04-06 9:53 AM, "Alexis"<[hidden email]>  wrote:
>
>> Hello
>>
>> I was reading some of my logs and found something strange :
>>
>>           at
>> org.biomart.configurator.controller.MartController.constructMartRegsitry(MartC
>> ontroller.java:1672)
>>
>> it's a mislocation of letters at Regsitry
>>
>> A definition of a Regsitry can be found at
>>
>> ./src/org/biomart/configurator/controller/MartController.java:  private
>> void constructMartRegsitry(MartRegistry registry, Element registryElement) {
>>
>> Is it controlled?? do you have a biohazard container around it :) ???
>>
>>      thanks
>>
>> Alexis
>>
>> ....biomart-path.../logs>  head stdouterr.2011_04_05.log
>> 2011-04-05 10:01:24,389 INFO  [main:Log.java:153]: Loading resources
>> from org/biomart/configurator/resources/messages
>> 2011-04-05 10:01:24,401 INFO  [main:Log.java:153]: Done loading resources
>> 2011-04-05 10:01:31,013 ERROR [main:Log.java:197]: null column
>> org.biomart.common.exceptions.AssociationException: The two keys cant be
>> related as they dont share the same number of columns.
>>           at
>> org.biomart.objects.objects.Relation.setStatus(Relation.java:262)
>>           at
>> org.biomart.objects.objects.Relation.synchronizedFromXML(Relation.java:552)
>>           at
>> org.biomart.objects.objects.Mart.synchronizedFromXML(Mart.java:694)
>>           at
>> org.biomart.objects.objects.MartRegistry.synchronizedFromXML(MartRegistry.java
>> :228)
>>           at
>> org.biomart.configurator.controller.MartController.constructMartRegsitry(MartC
>> ontroller.java:1672)
>>           at
>> org.biomart.configurator.controller.MartController.requestCreateRegistryFromXM
>> L(MartController.java:1649)
>>
>>
>> WARNING / LEGAL TEXT: This message is intended only for the use of the
>> individual or entity to which it is addressed and may contain
>> information which is privileged, confidential, proprietary, or exempt
>> from disclosure under applicable law. If you are not the intended
>> recipient or the person responsible for delivering the message to the
>> intended recipient, you are strictly prohibited from disclosing,
>> distributing, copying, or in any way using this message. If you have
>> received this communication in error, please notify the sender and
>> destroy and delete any copies you may have received.
>>
>> http://www.bsc.es/disclaimer.htm
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>
>


WARNING / LEGAL TEXT: This message is intended only for the use of the
individual or entity to which it is addressed and may contain
information which is privileged, confidential, proprietary, or exempt
from disclosure under applicable law. If you are not the intended
recipient or the person responsible for delivering the message to the
intended recipient, you are strictly prohibited from disclosing,
distributing, copying, or in any way using this message. If you have
received this communication in error, please notify the sender and
destroy and delete any copies you may have received.

http://www.bsc.es/disclaimer.htm
_______________________________________________
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Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5)

Junjun Zhang
In reply to this post by Jorge Zamora-2
Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5) Hi Jorge,

There is no additional installation is needed.

>From what you describe I am not quite sure what exactly the problem with KEGG pathways. Is there any chance I can access your server?

Thanks,
Junjun


On 11-04-07 5:25 AM, "Jorge Zamora" <jazamora@...> wrote:

Hi Junjun,

I've fully installed rc5, reconfigured icgc3.xml and It makes no
difference. It seems to me that the icgc3.xml that comes with the
installation has a different configuration compared to the one displayed
at http://dcc.icgc.org/, at least in the filter section of the
'ANYLISIS' and 'DATABASE SEARCH'.

Also, is there any graphic library that we should additionally install
to visualize the histograms/bars when resquesting KEGG pathways? I just
ask this since we have set up our local ICGC mart in two independent
machines. In both cases we tell there are differences in the
configuration compared to http://dcc.icgc.org/. However one only machine
displays KEGG pathways. That's why we're where suspecting there're
missing graphic libraries.

Thanks,
Jorge



Junjun Zhang wrote:
> Hi Jorge,
>
> We were trying to reproduce the problems at our side, but couldn’t get
> what you experienced. The problem might be caused by running incorrect
> UPDATE. We are developing a command line UPDATE tool for ICGC members,
> the tool will automate the operation as much as possible to minimize
> the chance of such type of errors.
>
> Best,
> Junjun
>
>
> On 11-04-05 5:35 AM, "Jorge Zamora" <jazamora@...> wrote:
>
>     Hello,
>
>     We have realized of some differences from our local ICGC mart with
>     respect to the web menu for other countries. We're using the icgc xml
>     that came with rc5. Specifically we're missing the following fields in
>     the web site:
>
>     - 'Gene type' and 'Mutation type' in ANALYSIS within both the
>     'Affected
>     Genes' and 'Affected Pathways' sections.
>     - 'Gene type' in DATABASE SEARCH within 'Genes' section.
>
>     is there any extra configuration needed in martconfigurator to display
>     this information?
>
>     Thanks
>     Jorge
>
>     **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso
>     los ficheros adjuntos, pueden contener información protegida para
>     el uso exclusivo de su destinatario. Se prohíbe la distribución,
>     reproducción o cualquier otro tipo de transmisión por parte de
>     otra persona que no sea el destinatario. Si usted recibe por error
>     este correo, se ruega comunicarlo al remitente y borrar el mensaje
>     recibido.
>     **CONFIDENTIALITY NOTICE** This email communication and any
>     attachments may contain confidential and privileged information
>     for the sole use of the designated recipient named above.
>     Distribution, reproduction or any other use of this transmission
>     by any party other than the intended recipient is prohibited. If
>     you are not the intended recipient please contact the sender and
>     delete all copies.
>
>     _______________________________________________
>     Users mailing list
>     Users@...
>     https://lists.biomart.org/mailman/listinfo/users
>


**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.



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Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5)

Jorge Zamora-2
Hi Junjun,

You mean the web server or the actual mart database.

Thanks,
Jorge

Junjun Zhang wrote:

> Hi Jorge,
>
> There is no additional installation is needed.
>
> From what you describe I am not quite sure what exactly the problem
> with KEGG pathways. Is there any chance I can access your server?
>
> Thanks,
> Junjun
>
>
> On 11-04-07 5:25 AM, "Jorge Zamora" <[hidden email]> wrote:
>
>     Hi Junjun,
>
>     I've fully installed rc5, reconfigured icgc3.xml and It makes no
>     difference. It seems to me that the icgc3.xml that comes with the
>     installation has a different configuration compared to the one
>     displayed
>     at http://dcc.icgc.org/, at least in the filter section of the
>     'ANYLISIS' and 'DATABASE SEARCH'.
>
>     Also, is there any graphic library that we should additionally install
>     to visualize the histograms/bars when resquesting KEGG pathways? I
>     just
>     ask this since we have set up our local ICGC mart in two independent
>     machines. In both cases we tell there are differences in the
>     configuration compared to http://dcc.icgc.org/. However one only
>     machine
>     displays KEGG pathways. That's why we're where suspecting there're
>     missing graphic libraries.
>
>     Thanks,
>     Jorge
>
>
>
>     Junjun Zhang wrote:
>     > Hi Jorge,
>     >
>     > We were trying to reproduce the problems at our side, but
>     couldn’t get
>     > what you experienced. The problem might be caused by running
>     incorrect
>     > UPDATE. We are developing a command line UPDATE tool for ICGC
>     members,
>     > the tool will automate the operation as much as possible to minimize
>     > the chance of such type of errors.
>     >
>     > Best,
>     > Junjun
>     >
>     >
>     > On 11-04-05 5:35 AM, "Jorge Zamora" <[hidden email]> wrote:
>     >
>     > Hello,
>     >
>     > We have realized of some differences from our local ICGC mart with
>     > respect to the web menu for other countries. We're using the icgc xml
>     > that came with rc5. Specifically we're missing the following
>     fields in
>     > the web site:
>     >
>     > - 'Gene type' and 'Mutation type' in ANALYSIS within both the
>     > 'Affected
>     > Genes' and 'Affected Pathways' sections.
>     > - 'Gene type' in DATABASE SEARCH within 'Genes' section.
>     >
>     > is there any extra configuration needed in martconfigurator to
>     display
>     > this information?
>     >
>     > Thanks
>     > Jorge
>     >
>     > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso
>     > los ficheros adjuntos, pueden contener información protegida para
>     > el uso exclusivo de su destinatario. Se prohíbe la distribución,
>     > reproducción o cualquier otro tipo de transmisión por parte de
>     > otra persona que no sea el destinatario. Si usted recibe por error
>     > este correo, se ruega comunicarlo al remitente y borrar el mensaje
>     > recibido.
>     > **CONFIDENTIALITY NOTICE** This email communication and any
>     > attachments may contain confidential and privileged information
>     > for the sole use of the designated recipient named above.
>     > Distribution, reproduction or any other use of this transmission
>     > by any party other than the intended recipient is prohibited. If
>     > you are not the intended recipient please contact the sender and
>     > delete all copies.
>     >
>     > _______________________________________________
>     > Users mailing list
>     > [hidden email]
>     > https://lists.biomart.org/mailman/listinfo/users
>     >
>
>
>     **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso
>     los ficheros adjuntos, pueden contener información protegida para
>     el uso exclusivo de su destinatario. Se prohíbe la distribución,
>     reproducción o cualquier otro tipo de transmisión por parte de
>     otra persona que no sea el destinatario. Si usted recibe por error
>     este correo, se ruega comunicarlo al remitente y borrar el mensaje
>     recibido.
>     **CONFIDENTIALITY NOTICE** This email communication and any
>     attachments may contain confidential and privileged information
>     for the sole use of the designated recipient named above.
>     Distribution, reproduction or any other use of this transmission
>     by any party other than the intended recipient is prohibited. If
>     you are not the intended recipient please contact the sender and
>     delete all copies.
>
>


**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5)

Junjun Zhang
Re: [BioMart Users] ANALYSIS and DATABASE SEARCH fields missing in local ICGC mart (rc5) The biomart web server. If it’s not accessible, some screenshots will help as well.


On 11-04-07 10:45 AM, "Jorge Zamora" <jazamora@...> wrote:

Hi Junjun,

You mean the web server or the actual mart database.

Thanks,
Jorge

Junjun Zhang wrote:
> Hi Jorge,
>
> There is no additional installation is needed.
>
> From what you describe I am not quite sure what exactly the problem
> with KEGG pathways. Is there any chance I can access your server?
>
> Thanks,
> Junjun
>
>
> On 11-04-07 5:25 AM, "Jorge Zamora" <jazamora@...> wrote:
>
>     Hi Junjun,
>
>     I've fully installed rc5, reconfigured icgc3.xml and It makes no
>     difference. It seems to me that the icgc3.xml that comes with the
>     installation has a different configuration compared to the one
>     displayed
>     at http://dcc.icgc.org/, at least in the filter section of the
>     'ANYLISIS' and 'DATABASE SEARCH'.
>
>     Also, is there any graphic library that we should additionally install
>     to visualize the histograms/bars when resquesting KEGG pathways? I
>     just
>     ask this since we have set up our local ICGC mart in two independent
>     machines. In both cases we tell there are differences in the
>     configuration compared to http://dcc.icgc.org/. However one only
>     machine
>     displays KEGG pathways. That's why we're where suspecting there're
>     missing graphic libraries.
>
>     Thanks,
>     Jorge
>
>
>
>     Junjun Zhang wrote:
>     > Hi Jorge,
>     >
>     > We were trying to reproduce the problems at our side, but
>     couldn’t get
>     > what you experienced. The problem might be caused by running
>     incorrect
>     > UPDATE. We are developing a command line UPDATE tool for ICGC
>     members,
>     > the tool will automate the operation as much as possible to minimize
>     > the chance of such type of errors.
>     >
>     > Best,
>     > Junjun
>     >
>     >
>     > On 11-04-05 5:35 AM, "Jorge Zamora" <jazamora@...> wrote:
>     >
>     > Hello,
>     >
>     > We have realized of some differences from our local ICGC mart with
>     > respect to the web menu for other countries. We're using the icgc xml
>     > that came with rc5. Specifically we're missing the following
>     fields in
>     > the web site:
>     >
>     > - 'Gene type' and 'Mutation type' in ANALYSIS within both the
>     > 'Affected
>     > Genes' and 'Affected Pathways' sections.
>     > - 'Gene type' in DATABASE SEARCH within 'Genes' section.
>     >
>     > is there any extra configuration needed in martconfigurator to
>     display
>     > this information?
>     >
>     > Thanks
>     > Jorge
>     >
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