[BioMart Users] moving marts from 0.7 to 0.8

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[BioMart Users] moving marts from 0.7 to 0.8

Richard Easty
Hi,

This is just a quick question about moving existing marts from 0.7 to 0.8

Apologies in advance, but I'm new to biomart, and have been asked to
check out what's involved in moving from 0.7 to 0.8

Could you tell me if there's some documentation that discusses this? I've
been using 'BioMart 0.8 User Manual - release candidate 6 - May, 2011'

I managed to load our 0.7 marts into martconfigurator 0.8, (via add
source/RDBMS pointing at the existing marts & using existing
config/add) but have not found a way to make changes and apply them.
I tried to edit an attribute name, then call update, then restart the
server with no change

I tried Materialize to generate the SQL, but get an
exception (IndexOutOfBounds) whether I aim it at file, text
editor or martrunner

Any advice would be very welcome

Regards

Richard Easty
Team87 WTSI



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 company registered in England with number 2742969, whose registered
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Re: [BioMart Users] moving marts from 0.7 to 0.8

Syed Haider-2
Hi Richard,


On 29/09/2011 18:09, Richard Easty wrote:
> Hi,
>
> This is just a quick question about moving existing marts from 0.7 to 0.8
>
> Apologies in advance, but I'm new to biomart, and have been asked to
> check out what's involved in moving from 0.7 to 0.8
>
> Could you tell me if there's some documentation that discusses this? I've
> been using 'BioMart 0.8 User Manual - release candidate 6 - May, 2011'

you are using the correct documentation.

>
> I managed to load our 0.7 marts into martconfigurator 0.8, (via add
> source/RDBMS pointing at the existing marts&  using existing
> config/add) but have not found a way to make changes and apply them.
> I tried to edit an attribute name, then call update, then restart the
> server with no change

please see section 5.8. Dont use update for this, Update refers to
updating configuration based on underlying database changes. good you
brought this up, the terms are slightly confusing.

>
> I tried Materialize to generate the SQL, but get an
> exception (IndexOutOfBounds) whether I aim it at file, text
> editor or martrunner

Perhaps you do not need this. As i understand, your already have a mart,
hence no point materialising it. Materialise is for converting a
non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run this on
your mart. However, the exception definitely needs to be handled
gracefully. Its a release candidate after all :)

HTH,
Syed

> Any advice would be very welcome
>
> Regards
>
> Richard Easty
> Team87 WTSI
>
>
>
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Re: [BioMart Users] moving marts from 0.7 to 0.8

Richard Easty
Hi Syed

Thanks for your reply - you will have to excuse my ham-fisted attempts at
getting to grips with biomart!

As far as I can tell, 5.8 describes access points & how to modify filters
and attributes which I am OK with so far

Having loaded one of our marts, (and following 5.8) I inspected what was
in 0.8's martConfigurator and it appeared to match what was in 0.7's
martEditor

My issue is with applying any changes to the mart using 0.8 such that they
are reflected in the web interface

In 0.7's ME I think Update was the menuitem I used, or Upload All to apply
all the XML before restarting the server hence my false starts with Update
& Materialize

Is there a similar process in 0.8 or (very likely) am I missing something
crucial?

Regards

Richard

On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider <[hidden email]> wrote:
> Hi Richard,
>
>
> On 29/09/2011 18:09, Richard Easty wrote:
>> Hi,
>>
>> This is just a quick question about moving existing marts from 0.7 to
0.8
>>
>> Apologies in advance, but I'm new to biomart, and have been asked to
>> check out what's involved in moving from 0.7 to 0.8
>>
>> Could you tell me if there's some documentation that discusses this?
I've

>> been using 'BioMart 0.8 User Manual - release candidate 6 - May, 2011'
>
> you are using the correct documentation.
>
>>
>> I managed to load our 0.7 marts into martconfigurator 0.8, (via add
>> source/RDBMS pointing at the existing marts&  using existing
>> config/add) but have not found a way to make changes and apply them.
>> I tried to edit an attribute name, then call update, then restart the
>> server with no change
>
> please see section 5.8. Dont use update for this, Update refers to
> updating configuration based on underlying database changes. good you
> brought this up, the terms are slightly confusing.
>
>>
>> I tried Materialize to generate the SQL, but get an
>> exception (IndexOutOfBounds) whether I aim it at file, text
>> editor or martrunner
>
> Perhaps you do not need this. As i understand, your already have a mart,

> hence no point materialising it. Materialise is for converting a
> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run this on

> your mart. However, the exception definitely needs to be handled
> gracefully. Its a release candidate after all :)
>
> HTH,
> Syed
>
>> Any advice would be very welcome
>>
>> Regards
>>
>> Richard Easty
>> Team87 WTSI
>>
>>
>>



--
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 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.
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Re: [BioMart Users] moving marts from 0.7 to 0.8

Syed Haider
Hi Richard,

On 30/09/2011 09:01, Richard Easty wrote:

> Hi Syed
>
> Thanks for your reply - you will have to excuse my ham-fisted attempts at
> getting to grips with biomart!
>
> As far as I can tell, 5.8 describes access points&  how to modify filters
> and attributes which I am OK with so far
>
> Having loaded one of our marts, (and following 5.8) I inspected what was
> in 0.8's martConfigurator and it appeared to match what was in 0.7's
> martEditor
>
> My issue is with applying any changes to the mart using 0.8 such that they
> are reflected in the web interface
>
> In 0.7's ME I think Update was the menuitem I used, or Upload All to apply
> all the XML before restarting the server hence my false starts with Update
> &  Materialize

In v0.7, any configuration changes are saved to XML using 'Export' and
to have these reflected in the web interface, you would redo perl
bin/configure... followed by apache restart. In v0.8, just use the
File->save option and then restart jetty.

>
> Is there a similar process in 0.8 or (very likely) am I missing something
> crucial?
>
> Regards
>
> Richard
>
> On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider<[hidden email]>  wrote:
>> Hi Richard,
>>
>>
>> On 29/09/2011 18:09, Richard Easty wrote:
>>> Hi,
>>>
>>> This is just a quick question about moving existing marts from 0.7 to
> 0.8
>>>
>>> Apologies in advance, but I'm new to biomart, and have been asked to
>>> check out what's involved in moving from 0.7 to 0.8
>>>
>>> Could you tell me if there's some documentation that discusses this?
> I've
>>> been using 'BioMart 0.8 User Manual - release candidate 6 - May, 2011'
>>
>> you are using the correct documentation.
>>
>>>
>>> I managed to load our 0.7 marts into martconfigurator 0.8, (via add
>>> source/RDBMS pointing at the existing marts&   using existing
>>> config/add) but have not found a way to make changes and apply them.
>>> I tried to edit an attribute name, then call update, then restart the
>>> server with no change
>>
>> please see section 5.8. Dont use update for this, Update refers to
>> updating configuration based on underlying database changes. good you
>> brought this up, the terms are slightly confusing.
>>
>>>
>>> I tried Materialize to generate the SQL, but get an
>>> exception (IndexOutOfBounds) whether I aim it at file, text
>>> editor or martrunner
>>
>> Perhaps you do not need this. As i understand, your already have a mart,
>
>> hence no point materialising it. Materialise is for converting a
>> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run this on
>
>> your mart. However, the exception definitely needs to be handled
>> gracefully. Its a release candidate after all :)
>>
>> HTH,
>> Syed
>>
>>> Any advice would be very welcome
>>>
>>> Regards
>>>
>>> Richard Easty
>>> Team87 WTSI
>>>
>>>
>>>
>
>
>
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Re: [BioMart Users] moving marts from 0.7 to 0.8

Christophe Klopp
Hi Richard and Syed,

To follow up with Richards' question about importing from 0.7 to 0.8, Is
it possible to retrieve directly all the user interface done on mart0.7
in 0.8?
For example by reading the compressed XML which is in the database?

Cheers

Christophe


Le 30/09/2011 12:00, Syed Haider a écrit :

> Hi Richard,
>
> On 30/09/2011 09:01, Richard Easty wrote:
>> Hi Syed
>>
>> Thanks for your reply - you will have to excuse my ham-fisted
>> attempts at
>> getting to grips with biomart!
>>
>> As far as I can tell, 5.8 describes access points&  how to modify
>> filters
>> and attributes which I am OK with so far
>>
>> Having loaded one of our marts, (and following 5.8) I inspected what was
>> in 0.8's martConfigurator and it appeared to match what was in 0.7's
>> martEditor
>>
>> My issue is with applying any changes to the mart using 0.8 such that
>> they
>> are reflected in the web interface
>>
>> In 0.7's ME I think Update was the menuitem I used, or Upload All to
>> apply
>> all the XML before restarting the server hence my false starts with
>> Update
>> &  Materialize
>
> In v0.7, any configuration changes are saved to XML using 'Export' and
> to have these reflected in the web interface, you would redo perl
> bin/configure... followed by apache restart. In v0.8, just use the
> File->save option and then restart jetty.
>
>>
>> Is there a similar process in 0.8 or (very likely) am I missing
>> something
>> crucial?
>>
>> Regards
>>
>> Richard
>>
>> On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider<[hidden email]>  wrote:
>>> Hi Richard,
>>>
>>>
>>> On 29/09/2011 18:09, Richard Easty wrote:
>>>> Hi,
>>>>
>>>> This is just a quick question about moving existing marts from 0.7 to
>> 0.8
>>>>
>>>> Apologies in advance, but I'm new to biomart, and have been asked to
>>>> check out what's involved in moving from 0.7 to 0.8
>>>>
>>>> Could you tell me if there's some documentation that discusses this?
>> I've
>>>> been using 'BioMart 0.8 User Manual - release candidate 6 - May, 2011'
>>>
>>> you are using the correct documentation.
>>>
>>>>
>>>> I managed to load our 0.7 marts into martconfigurator 0.8, (via add
>>>> source/RDBMS pointing at the existing marts&   using existing
>>>> config/add) but have not found a way to make changes and apply them.
>>>> I tried to edit an attribute name, then call update, then restart the
>>>> server with no change
>>>
>>> please see section 5.8. Dont use update for this, Update refers to
>>> updating configuration based on underlying database changes. good you
>>> brought this up, the terms are slightly confusing.
>>>
>>>>
>>>> I tried Materialize to generate the SQL, but get an
>>>> exception (IndexOutOfBounds) whether I aim it at file, text
>>>> editor or martrunner
>>>
>>> Perhaps you do not need this. As i understand, your already have a
>>> mart,
>>
>>> hence no point materialising it. Materialise is for converting a
>>> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run
>>> this on
>>
>>> your mart. However, the exception definitely needs to be handled
>>> gracefully. Its a release candidate after all :)
>>>
>>> HTH,
>>> Syed
>>>
>>>> Any advice would be very welcome
>>>>
>>>> Regards
>>>>
>>>> Richard Easty
>>>> Team87 WTSI
>>>>
>>>>
>>>>
>>
>>
>>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users

--
====================================================================
= Christophe KLOPP BIA    INRA Toulouse 31326 Castanet-Tolosan     =
= Tel: 33 5 61 28 50 36   Email: [hidden email] =
= http://www.sigenae.org/                                          =
= http://bioinfo.genotoul.fr/                                      =
====================================================================

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Re: [BioMart Users] moving marts from 0.7 to 0.8

Syed Haider-2
Hi Christophe,

Yes, it should be able to recover almost all of it if you connect it to
Type=RDBMS and say Yes to popup (documentation ref: 5.4 Adding a new
RDBMS Source)

Best,
Syed

On 30/09/2011 13:28, Christophe Klopp wrote:

> Hi Richard and Syed,
>
> To follow up with Richards' question about importing from 0.7 to 0.8, Is
> it possible to retrieve directly all the user interface done on mart0.7
> in 0.8?
> For example by reading the compressed XML which is in the database?
>
> Cheers
>
> Christophe
>
>
> Le 30/09/2011 12:00, Syed Haider a écrit :
>> Hi Richard,
>>
>> On 30/09/2011 09:01, Richard Easty wrote:
>>> Hi Syed
>>>
>>> Thanks for your reply - you will have to excuse my ham-fisted
>>> attempts at
>>> getting to grips with biomart!
>>>
>>> As far as I can tell, 5.8 describes access points&   how to modify
>>> filters
>>> and attributes which I am OK with so far
>>>
>>> Having loaded one of our marts, (and following 5.8) I inspected what was
>>> in 0.8's martConfigurator and it appeared to match what was in 0.7's
>>> martEditor
>>>
>>> My issue is with applying any changes to the mart using 0.8 such that
>>> they
>>> are reflected in the web interface
>>>
>>> In 0.7's ME I think Update was the menuitem I used, or Upload All to
>>> apply
>>> all the XML before restarting the server hence my false starts with
>>> Update
>>> &   Materialize
>>
>> In v0.7, any configuration changes are saved to XML using 'Export' and
>> to have these reflected in the web interface, you would redo perl
>> bin/configure... followed by apache restart. In v0.8, just use the
>> File->save option and then restart jetty.
>>
>>>
>>> Is there a similar process in 0.8 or (very likely) am I missing
>>> something
>>> crucial?
>>>
>>> Regards
>>>
>>> Richard
>>>
>>> On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider<[hidden email]>   wrote:
>>>> Hi Richard,
>>>>
>>>>
>>>> On 29/09/2011 18:09, Richard Easty wrote:
>>>>> Hi,
>>>>>
>>>>> This is just a quick question about moving existing marts from 0.7 to
>>> 0.8
>>>>>
>>>>> Apologies in advance, but I'm new to biomart, and have been asked to
>>>>> check out what's involved in moving from 0.7 to 0.8
>>>>>
>>>>> Could you tell me if there's some documentation that discusses this?
>>> I've
>>>>> been using 'BioMart 0.8 User Manual - release candidate 6 - May, 2011'
>>>>
>>>> you are using the correct documentation.
>>>>
>>>>>
>>>>> I managed to load our 0.7 marts into martconfigurator 0.8, (via add
>>>>> source/RDBMS pointing at the existing marts&    using existing
>>>>> config/add) but have not found a way to make changes and apply them.
>>>>> I tried to edit an attribute name, then call update, then restart the
>>>>> server with no change
>>>>
>>>> please see section 5.8. Dont use update for this, Update refers to
>>>> updating configuration based on underlying database changes. good you
>>>> brought this up, the terms are slightly confusing.
>>>>
>>>>>
>>>>> I tried Materialize to generate the SQL, but get an
>>>>> exception (IndexOutOfBounds) whether I aim it at file, text
>>>>> editor or martrunner
>>>>
>>>> Perhaps you do not need this. As i understand, your already have a
>>>> mart,
>>>
>>>> hence no point materialising it. Materialise is for converting a
>>>> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run
>>>> this on
>>>
>>>> your mart. However, the exception definitely needs to be handled
>>>> gracefully. Its a release candidate after all :)
>>>>
>>>> HTH,
>>>> Syed
>>>>
>>>>> Any advice would be very welcome
>>>>>
>>>>> Regards
>>>>>
>>>>> Richard Easty
>>>>> Team87 WTSI
>>>>>
>>>>>
>>>>>
>>>
>>>
>>>
>> _______________________________________________
>> Users mailing list
>> [hidden email]
>> https://lists.biomart.org/mailman/listinfo/users
>
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Re: [BioMart Users] moving marts from 0.7 to 0.8

Syed Haider-2

Hi Christoph,

Please try running it on:
host: martdb.ensembl.org
port: 5316
user: anonymous
pass:
database & schema: vega_mart_62

Best,
Syed



On 30/09/2011 16:02, Christophe Klopp wrote:

> Hi Syed,
>
> I've tried this solution and got the popup "Do you want to use the
> existing config" to which I answered yes. But nothing happened and no
> error message appeared on my terminal.
> I use a local 0.7 mart instance : http://sigreannot-mart.toulouse.inra.fr/
>
> Version of the mart code : release-0_8-candidate_7
>
> Is there a public database which works for you, I could try?
>
> Cheers
>
> Christophe
>
>
>
> Le 30/09/2011 16:22, Syed Haider a écrit :
>> Hi Christophe,
>>
>> Yes, it should be able to recover almost all of it if you connect it
>> to Type=RDBMS and say Yes to popup (documentation ref: 5.4 Adding a
>> new RDBMS Source)
>>
>> Best,
>> Syed
>>
>> On 30/09/2011 13:28, Christophe Klopp wrote:
>>> Hi Richard and Syed,
>>>
>>> To follow up with Richards' question about importing from 0.7 to 0.8, Is
>>> it possible to retrieve directly all the user interface done on mart0.7
>>> in 0.8?
>>> For example by reading the compressed XML which is in the database?
>>>
>>> Cheers
>>>
>>> Christophe
>>>
>>>
>>> Le 30/09/2011 12:00, Syed Haider a écrit :
>>>> Hi Richard,
>>>>
>>>> On 30/09/2011 09:01, Richard Easty wrote:
>>>>> Hi Syed
>>>>>
>>>>> Thanks for your reply - you will have to excuse my ham-fisted
>>>>> attempts at
>>>>> getting to grips with biomart!
>>>>>
>>>>> As far as I can tell, 5.8 describes access points& how to modify
>>>>> filters
>>>>> and attributes which I am OK with so far
>>>>>
>>>>> Having loaded one of our marts, (and following 5.8) I inspected
>>>>> what was
>>>>> in 0.8's martConfigurator and it appeared to match what was in 0.7's
>>>>> martEditor
>>>>>
>>>>> My issue is with applying any changes to the mart using 0.8 such that
>>>>> they
>>>>> are reflected in the web interface
>>>>>
>>>>> In 0.7's ME I think Update was the menuitem I used, or Upload All to
>>>>> apply
>>>>> all the XML before restarting the server hence my false starts with
>>>>> Update
>>>>> & Materialize
>>>>
>>>> In v0.7, any configuration changes are saved to XML using 'Export' and
>>>> to have these reflected in the web interface, you would redo perl
>>>> bin/configure... followed by apache restart. In v0.8, just use the
>>>> File->save option and then restart jetty.
>>>>
>>>>>
>>>>> Is there a similar process in 0.8 or (very likely) am I missing
>>>>> something
>>>>> crucial?
>>>>>
>>>>> Regards
>>>>>
>>>>> Richard
>>>>>
>>>>> On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider<[hidden email]>
>>>>> wrote:
>>>>>> Hi Richard,
>>>>>>
>>>>>>
>>>>>> On 29/09/2011 18:09, Richard Easty wrote:
>>>>>>> Hi,
>>>>>>>
>>>>>>> This is just a quick question about moving existing marts from
>>>>>>> 0.7 to
>>>>> 0.8
>>>>>>>
>>>>>>> Apologies in advance, but I'm new to biomart, and have been asked to
>>>>>>> check out what's involved in moving from 0.7 to 0.8
>>>>>>>
>>>>>>> Could you tell me if there's some documentation that discusses this?
>>>>> I've
>>>>>>> been using 'BioMart 0.8 User Manual - release candidate 6 - May,
>>>>>>> 2011'
>>>>>>
>>>>>> you are using the correct documentation.
>>>>>>
>>>>>>>
>>>>>>> I managed to load our 0.7 marts into martconfigurator 0.8, (via add
>>>>>>> source/RDBMS pointing at the existing marts& using existing
>>>>>>> config/add) but have not found a way to make changes and apply them.
>>>>>>> I tried to edit an attribute name, then call update, then restart
>>>>>>> the
>>>>>>> server with no change
>>>>>>
>>>>>> please see section 5.8. Dont use update for this, Update refers to
>>>>>> updating configuration based on underlying database changes. good you
>>>>>> brought this up, the terms are slightly confusing.
>>>>>>
>>>>>>>
>>>>>>> I tried Materialize to generate the SQL, but get an
>>>>>>> exception (IndexOutOfBounds) whether I aim it at file, text
>>>>>>> editor or martrunner
>>>>>>
>>>>>> Perhaps you do not need this. As i understand, your already have a
>>>>>> mart,
>>>>>
>>>>>> hence no point materialising it. Materialise is for converting a
>>>>>> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run
>>>>>> this on
>>>>>
>>>>>> your mart. However, the exception definitely needs to be handled
>>>>>> gracefully. Its a release candidate after all :)
>>>>>>
>>>>>> HTH,
>>>>>> Syed
>>>>>>
>>>>>>> Any advice would be very welcome
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> Richard Easty
>>>>>>> Team87 WTSI
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> Users mailing list
>>>> [hidden email]
>>>> https://lists.biomart.org/mailman/listinfo/users
>>>
>
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Re: [BioMart Users] moving marts from 0.7 to 0.8

Syed Haider-2
Hi Christophe,

Well, i can only guess that there seems to be a problem that backward
compatability is unable to handle at this stage. I wonder if it works
for you if you use release-0_8-candidate_6 or release-0_8-candidate_5 ?

Syed


On 30/09/2011 16:28, Christophe Klopp wrote:

> It works fine!
> Any Idea of what could be the problem with our database?
>
> Cheers
>
> Christophe
>
>
>
> Le 30/09/2011 17:05, Syed Haider a écrit :
>>
>> Hi Christoph,
>>
>> Please try running it on:
>> host: martdb.ensembl.org
>> port: 5316
>> user: anonymous
>> pass:
>> database & schema: vega_mart_62
>>
>> Best,
>> Syed
>>
>>
>>
>> On 30/09/2011 16:02, Christophe Klopp wrote:
>>> Hi Syed,
>>>
>>> I've tried this solution and got the popup "Do you want to use the
>>> existing config" to which I answered yes. But nothing happened and no
>>> error message appeared on my terminal.
>>> I use a local 0.7 mart instance :
>>> http://sigreannot-mart.toulouse.inra.fr/
>>>
>>> Version of the mart code : release-0_8-candidate_7
>>>
>>> Is there a public database which works for you, I could try?
>>>
>>> Cheers
>>>
>>> Christophe
>>>
>>>
>>>
>>> Le 30/09/2011 16:22, Syed Haider a écrit :
>>>> Hi Christophe,
>>>>
>>>> Yes, it should be able to recover almost all of it if you connect it
>>>> to Type=RDBMS and say Yes to popup (documentation ref: 5.4 Adding a
>>>> new RDBMS Source)
>>>>
>>>> Best,
>>>> Syed
>>>>
>>>> On 30/09/2011 13:28, Christophe Klopp wrote:
>>>>> Hi Richard and Syed,
>>>>>
>>>>> To follow up with Richards' question about importing from 0.7 to
>>>>> 0.8, Is
>>>>> it possible to retrieve directly all the user interface done on
>>>>> mart0.7
>>>>> in 0.8?
>>>>> For example by reading the compressed XML which is in the database?
>>>>>
>>>>> Cheers
>>>>>
>>>>> Christophe
>>>>>
>>>>>
>>>>> Le 30/09/2011 12:00, Syed Haider a écrit :
>>>>>> Hi Richard,
>>>>>>
>>>>>> On 30/09/2011 09:01, Richard Easty wrote:
>>>>>>> Hi Syed
>>>>>>>
>>>>>>> Thanks for your reply - you will have to excuse my ham-fisted
>>>>>>> attempts at
>>>>>>> getting to grips with biomart!
>>>>>>>
>>>>>>> As far as I can tell, 5.8 describes access points& how to modify
>>>>>>> filters
>>>>>>> and attributes which I am OK with so far
>>>>>>>
>>>>>>> Having loaded one of our marts, (and following 5.8) I inspected
>>>>>>> what was
>>>>>>> in 0.8's martConfigurator and it appeared to match what was in 0.7's
>>>>>>> martEditor
>>>>>>>
>>>>>>> My issue is with applying any changes to the mart using 0.8 such
>>>>>>> that
>>>>>>> they
>>>>>>> are reflected in the web interface
>>>>>>>
>>>>>>> In 0.7's ME I think Update was the menuitem I used, or Upload All to
>>>>>>> apply
>>>>>>> all the XML before restarting the server hence my false starts with
>>>>>>> Update
>>>>>>> & Materialize
>>>>>>
>>>>>> In v0.7, any configuration changes are saved to XML using 'Export'
>>>>>> and
>>>>>> to have these reflected in the web interface, you would redo perl
>>>>>> bin/configure... followed by apache restart. In v0.8, just use the
>>>>>> File->save option and then restart jetty.
>>>>>>
>>>>>>>
>>>>>>> Is there a similar process in 0.8 or (very likely) am I missing
>>>>>>> something
>>>>>>> crucial?
>>>>>>>
>>>>>>> Regards
>>>>>>>
>>>>>>> Richard
>>>>>>>
>>>>>>> On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider<[hidden email]>
>>>>>>> wrote:
>>>>>>>> Hi Richard,
>>>>>>>>
>>>>>>>>
>>>>>>>> On 29/09/2011 18:09, Richard Easty wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> This is just a quick question about moving existing marts from
>>>>>>>>> 0.7 to
>>>>>>> 0.8
>>>>>>>>>
>>>>>>>>> Apologies in advance, but I'm new to biomart, and have been
>>>>>>>>> asked to
>>>>>>>>> check out what's involved in moving from 0.7 to 0.8
>>>>>>>>>
>>>>>>>>> Could you tell me if there's some documentation that discusses
>>>>>>>>> this?
>>>>>>> I've
>>>>>>>>> been using 'BioMart 0.8 User Manual - release candidate 6 - May,
>>>>>>>>> 2011'
>>>>>>>>
>>>>>>>> you are using the correct documentation.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> I managed to load our 0.7 marts into martconfigurator 0.8, (via
>>>>>>>>> add
>>>>>>>>> source/RDBMS pointing at the existing marts& using existing
>>>>>>>>> config/add) but have not found a way to make changes and apply
>>>>>>>>> them.
>>>>>>>>> I tried to edit an attribute name, then call update, then restart
>>>>>>>>> the
>>>>>>>>> server with no change
>>>>>>>>
>>>>>>>> please see section 5.8. Dont use update for this, Update refers to
>>>>>>>> updating configuration based on underlying database changes.
>>>>>>>> good you
>>>>>>>> brought this up, the terms are slightly confusing.
>>>>>>>>
>>>>>>>>>
>>>>>>>>> I tried Materialize to generate the SQL, but get an
>>>>>>>>> exception (IndexOutOfBounds) whether I aim it at file, text
>>>>>>>>> editor or martrunner
>>>>>>>>
>>>>>>>> Perhaps you do not need this. As i understand, your already have a
>>>>>>>> mart,
>>>>>>>
>>>>>>>> hence no point materialising it. Materialise is for converting a
>>>>>>>> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run
>>>>>>>> this on
>>>>>>>
>>>>>>>> your mart. However, the exception definitely needs to be handled
>>>>>>>> gracefully. Its a release candidate after all :)
>>>>>>>>
>>>>>>>> HTH,
>>>>>>>> Syed
>>>>>>>>
>>>>>>>>> Any advice would be very welcome
>>>>>>>>>
>>>>>>>>> Regards
>>>>>>>>>
>>>>>>>>> Richard Easty
>>>>>>>>> Team87 WTSI
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> _______________________________________________
>>>>>> Users mailing list
>>>>>> [hidden email]
>>>>>> https://lists.biomart.org/mailman/listinfo/users
>>>>>
>>>
>
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Re: [BioMart Users] moving marts from 0.7 to 0.8

Richard Easty
In reply to this post by Syed Haider-2
Hi Guys,

Just to sum-up my experience

I couldn't get anything to run from martConfigurator & assumed I was
missing having installed something crucial

Turns out things were configured (mostly) right, but I couldn't start the
server from within martConfigurator without the error:

Invalid maximum heap size: -Xmx4096m

Few edits to biomart-server.sh (bringing down heap size) sorted that out

So I can't start from within martConfigurator, but can use
biomart-server.sh instead

Thanks again for your help

Cheers

Richard

On Fri, 30 Sep 2011 15:22:56 +0100, Syed Haider <[hidden email]> wrote:

> Hi Christophe,
>
> Yes, it should be able to recover almost all of it if you connect it to
> Type=RDBMS and say Yes to popup (documentation ref: 5.4 Adding a new
> RDBMS Source)
>
> Best,
> Syed
>
> On 30/09/2011 13:28, Christophe Klopp wrote:
>> Hi Richard and Syed,
>>
>> To follow up with Richards' question about importing from 0.7 to 0.8,
Is

>> it possible to retrieve directly all the user interface done on mart0.7
>> in 0.8?
>> For example by reading the compressed XML which is in the database?
>>
>> Cheers
>>
>> Christophe
>>
>>
>> Le 30/09/2011 12:00, Syed Haider a écrit :
>>> Hi Richard,
>>>
>>> On 30/09/2011 09:01, Richard Easty wrote:
>>>> Hi Syed
>>>>
>>>> Thanks for your reply - you will have to excuse my ham-fisted
>>>> attempts at
>>>> getting to grips with biomart!
>>>>
>>>> As far as I can tell, 5.8 describes access points&   how to modify
>>>> filters
>>>> and attributes which I am OK with so far
>>>>
>>>> Having loaded one of our marts, (and following 5.8) I inspected what
>>>> was
>>>> in 0.8's martConfigurator and it appeared to match what was in 0.7's
>>>> martEditor
>>>>
>>>> My issue is with applying any changes to the mart using 0.8 such that
>>>> they
>>>> are reflected in the web interface
>>>>
>>>> In 0.7's ME I think Update was the menuitem I used, or Upload All to
>>>> apply
>>>> all the XML before restarting the server hence my false starts with
>>>> Update
>>>> &   Materialize
>>>
>>> In v0.7, any configuration changes are saved to XML using 'Export' and
>>> to have these reflected in the web interface, you would redo perl
>>> bin/configure... followed by apache restart. In v0.8, just use the
>>> File->save option and then restart jetty.
>>>
>>>>
>>>> Is there a similar process in 0.8 or (very likely) am I missing
>>>> something
>>>> crucial?
>>>>
>>>> Regards
>>>>
>>>> Richard
>>>>
>>>> On Thu, 29 Sep 2011 19:38:54 +0100, Syed Haider<[hidden email]>  
>>>> wrote:
>>>>> Hi Richard,
>>>>>
>>>>>
>>>>> On 29/09/2011 18:09, Richard Easty wrote:
>>>>>> Hi,
>>>>>>
>>>>>> This is just a quick question about moving existing marts from 0.7
to
>>>> 0.8
>>>>>>
>>>>>> Apologies in advance, but I'm new to biomart, and have been asked
to
>>>>>> check out what's involved in moving from 0.7 to 0.8
>>>>>>
>>>>>> Could you tell me if there's some documentation that discusses
this?

>>>> I've
>>>>>> been using 'BioMart 0.8 User Manual - release candidate 6 - May,
>>>>>> 2011'
>>>>>
>>>>> you are using the correct documentation.
>>>>>
>>>>>>
>>>>>> I managed to load our 0.7 marts into martconfigurator 0.8, (via add
>>>>>> source/RDBMS pointing at the existing marts&    using existing
>>>>>> config/add) but have not found a way to make changes and apply
them.
>>>>>> I tried to edit an attribute name, then call update, then restart
the
>>>>>> server with no change
>>>>>
>>>>> please see section 5.8. Dont use update for this, Update refers to
>>>>> updating configuration based on underlying database changes. good
you

>>>>> brought this up, the terms are slightly confusing.
>>>>>
>>>>>>
>>>>>> I tried Materialize to generate the SQL, but get an
>>>>>> exception (IndexOutOfBounds) whether I aim it at file, text
>>>>>> editor or martrunner
>>>>>
>>>>> Perhaps you do not need this. As i understand, your already have a
>>>>> mart,
>>>>
>>>>> hence no point materialising it. Materialise is for converting a
>>>>> non-Biomart RDBMS to a Biomart RDBMS. Hence you dont need to run
>>>>> this on
>>>>
>>>>> your mart. However, the exception definitely needs to be handled
>>>>> gracefully. Its a release candidate after all :)
>>>>>
>>>>> HTH,
>>>>> Syed
>>>>>
>>>>>> Any advice would be very welcome
>>>>>>
>>>>>> Regards
>>>>>>
>>>>>> Richard Easty
>>>>>> Team87 WTSI
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> Users mailing list
>>> [hidden email]
>>> https://lists.biomart.org/mailman/listinfo/users
>>
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users


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