Re: setting up chado (tripal) intermine

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Re: setting up chado (tripal) intermine

Julie Sullivan
Hi Sofia!

All your files look fine to me. This line from the tutorial:

        (cd ../dbmodel && ant build-db -v); ant -Dsource=chado-db -v

Assumes that your source is called chado-db. You have named your source
in your project XML "drupal".

So try this instead:

        (cd ../dbmodel && ant build-db -v); ant -Dsource=drupal -v

Julie

----

Hello.

I am having issues trying to set up my intermine from a chado database
(actually a chado database within a tripal database).

I am following the steps in
http://intermine.readthedocs.org/en/latest/database/data-sources/library/chado/#index-0
but
feel as if I must be missing something.

ERROR:

BUILD FAILED
/data/src/intermine/imbuild/integrate.xml:54: can't find source in project
definition file: chado-db

my ~/.intermine/simrmine.properties:
db.flybase.datasource.class=org.postgresql.ds.PGPoolingDataSource
db.flybase.datasource.dataSourceName=db.flybase
db.flybase.datasource.serverName=localhost
db.flybase.datasource.port=5432
db.flybase.datasource.databaseName=drupal
db.flybase.datasource.user=xxxx
db.flybase.datasource.password=xxxx
db.flybase.datasource.maxCommections=10
db.flybase.datasource.driver=org.postgresql.Driver
db.flybase.datasource.platform=PostgreSql

my project.xml:
<source name="drupal" type="chado-db" dump="true">
   <property name="source.db.name" value="flybase"/>
   <property name="genus" value="Schmidtea"/>
   <property name="species" value="mediterranea"/>
   <property name="dataSourceName" value="Flybase"/>
   <property name="dataSetTitle" value="SmedSxl_v31 data set"/>
   <property name="converter.class"
value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
   <property name="processors"
value="org.intermine.bio.dataconversion.SequenceProcessor"/>
</source>

Thanks,
Sofia

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Re: setting up chado (tripal) intermine

vkrishna
Hi Sofia,

Another issue you will encounter when loading from a Tripal-based Chado database is that the Chado specific tables are not in the postgres default “public” schema of the database. Instead, Tripal puts it in a postgres schema named “chado".

To workaround this, you would need to alter your Chado processor to run the query “ALTER DATABASE <dbname> SET search_path TO chado, public” first, before running any SELECT statements.

Hope this helps!
Vivek

> On Dec 2, 2014, at 12:37 PM, Julie Sullivan <[hidden email]> wrote:
>
> Hi Sofia!
>
> All your files look fine to me. This line from the tutorial:
>
> (cd ../dbmodel && ant build-db -v); ant -Dsource=chado-db -v
>
> Assumes that your source is called chado-db. You have named your source
> in your project XML "drupal".
>
> So try this instead:
>
> (cd ../dbmodel && ant build-db -v); ant -Dsource=drupal -v
>
> Julie
>
> ----
>
> Hello.
>
> I am having issues trying to set up my intermine from a chado database
> (actually a chado database within a tripal database).
>
> I am following the steps in
> http://intermine.readthedocs.org/en/latest/database/data-sources/library/chado/#index-0
> but
> feel as if I must be missing something.
>
> ERROR:
>
> BUILD FAILED
> /data/src/intermine/imbuild/integrate.xml:54: can't find source in project
> definition file: chado-db
>
> my ~/.intermine/simrmine.properties:
> db.flybase.datasource.class=org.postgresql.ds.PGPoolingDataSource
> db.flybase.datasource.dataSourceName=db.flybase
> db.flybase.datasource.serverName=localhost
> db.flybase.datasource.port=5432
> db.flybase.datasource.databaseName=drupal
> db.flybase.datasource.user=xxxx
> db.flybase.datasource.password=xxxx
> db.flybase.datasource.maxCommections=10
> db.flybase.datasource.driver=org.postgresql.Driver
> db.flybase.datasource.platform=PostgreSql
>
> my project.xml:
> <source name="drupal" type="chado-db" dump="true">
>   <property name="source.db.name" value="flybase"/>
>   <property name="genus" value="Schmidtea"/>
>   <property name="species" value="mediterranea"/>
>   <property name="dataSourceName" value="Flybase"/>
>   <property name="dataSetTitle" value="SmedSxl_v31 data set"/>
>   <property name="converter.class"
> value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
>   <property name="processors"
> value="org.intermine.bio.dataconversion.SequenceProcessor"/>
> </source>
>
> Thanks,
> Sofia
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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Re: setting up chado (tripal) intermine

Sofia Robb
In reply to this post by Julie Sullivan
Hi Julie,
Thank you so much. I made the change and that error is gone, but now I have another

BUILD FAILED
/data/src/intermine/imbuild/library.xml:78: The following error occurred while executing this line:
/data/src/intermine/imbuild/objectstore.xml:93: java.lang.NullPointerException: Datasource is null. Properties are: {datasource.port=5432, datasource.user=intermine, platform=PostgreSQL, datasource.databaseName=simrmine, datasource.serverName=localhost, driver=org.postgresql.Driver, datasource.password=xxxx, datasource.maxConnections=50}

Here is the excerpt from my ~/.intermine/simrmine.properties

db.production.datasource.serverName=localhost
db.production.datasource.port=5432
db.production.datasource.databaseName=simrmine
db.production.datasource.user=intermine
db.production.datasource.password=xxxxx

I have no problems when log into the simrmine database manually with psql with the user intermine and the password. I double checked the port, and it is 5432. 

Thank you for your help!
Sofia 

On Tue, Dec 2, 2014 at 12:37 PM, Julie Sullivan <[hidden email]> wrote:
Hi Sofia!

All your files look fine to me. This line from the tutorial:

        (cd ../dbmodel && ant build-db -v); ant -Dsource=chado-db -v

Assumes that your source is called chado-db. You have named your source in your project XML "drupal".

So try this instead:

        (cd ../dbmodel && ant build-db -v); ant -Dsource=drupal -v

Julie

----


Hello.

I am having issues trying to set up my intermine from a chado database
(actually a chado database within a tripal database).

I am following the steps in
http://intermine.readthedocs.org/en/latest/database/data-sources/library/chado/#index-0
but
feel as if I must be missing something.

ERROR:

BUILD FAILED
/data/src/intermine/imbuild/integrate.xml:54: can't find source in project
definition file: chado-db

my ~/.intermine/simrmine.properties:
db.flybase.datasource.class=org.postgresql.ds.PGPoolingDataSource
db.flybase.datasource.dataSourceName=db.flybase
db.flybase.datasource.serverName=localhost
db.flybase.datasource.port=5432
db.flybase.datasource.databaseName=drupal
db.flybase.datasource.user=xxxx
db.flybase.datasource.password=xxxx
db.flybase.datasource.maxCommections=10
db.flybase.datasource.driver=org.postgresql.Driver
db.flybase.datasource.platform=PostgreSql

my project.xml:
<source name="drupal" type="chado-db" dump="true">
  <property name="source.db.name" value="flybase"/>
  <property name="genus" value="Schmidtea"/>
  <property name="species" value="mediterranea"/>
  <property name="dataSourceName" value="Flybase"/>
  <property name="dataSetTitle" value="SmedSxl_v31 data set"/>
  <property name="converter.class"
value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
  <property name="processors"
value="org.intermine.bio.dataconversion.SequenceProcessor"/>
</source>

Thanks,
Sofia


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Re: setting up chado (tripal) intermine

Julie Sullivan
In reply to this post by Julie Sullivan
Did you update the postgres pg_hba.conf file?

http://intermine.readthedocs.org/en/latest/system-requirements/software/postgres/postgres/

----

Hi Julie,
Thank you so much. I made the change and that error is gone, but now I
have another

BUILD FAILED
/data/src/intermine/imbuild/library.xml:78: The following error occurred
while executing this line:
/data/src/intermine/imbuild/objectstore.xml:93:
java.lang.NullPointerException: Datasource is null. Properties are:
{datasource.port=5432, datasource.user=intermine, platform=PostgreSQL,
datasource.databaseName=simrmine, datasource.serverName=localhost,
driver=org.postgresql.Driver, datasource.password=xxxx,
datasource.maxConnections=50}

Here is the excerpt from my ~/.intermine/simrmine.properties

db.production.datasource.serverName=localhost
db.production.datasource.port=5432
db.production.datasource.databaseName=simrmine
db.production.datasource.user=intermine
db.production.datasource.password=xxxxx

I have no problems when log into the simrmine database manually with
psql with the user intermine and the password. I double checked the
port, and it is 5432.

Thank you for your help!
Sofia


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Re: setting up chado (tripal) intermine

Sofia Robb
Hi Julie,

I added the line 
"host all all 0.0.0.0/0 password
to my pg_hba.conf file, stopped and restarted my postgres service and I still have this error:


BUILD FAILED
/data/src/intermine/imbuild/library.xml:78: The following error occurred while executing this line:
/data/src/intermine/imbuild/objectstore.xml:93: java.lang.NullPointerException: Datasource is null. Properties are: {datasource.port=5432, datasource.user=intermine, platform=PostgreSQL, datasource.databaseName=simrmine, datasource.serverName=localhost, driver=org.postgresql.Driver, datasource.password=xxxxx, datasource.maxConnections=50}

Thank you,
Sofia

On Mon, Dec 8, 2014 at 8:23 AM, Julie Sullivan <[hidden email]> wrote:
Did you update the postgres pg_hba.conf file?

http://intermine.readthedocs.org/en/latest/system-requirements/software/postgres/postgres/

----


Hi Julie,
Thank you so much. I made the change and that error is gone, but now I have another

BUILD FAILED
/data/src/intermine/imbuild/library.xml:78: The following error occurred while executing this line:
/data/src/intermine/imbuild/objectstore.xml:93: java.lang.NullPointerException: Datasource is null. Properties are: {datasource.port=5432, datasource.user=intermine, platform=PostgreSQL, datasource.databaseName=simrmine, datasource.serverName=localhost, driver=org.postgresql.Driver, datasource.password=xxxx, datasource.maxConnections=50}

Here is the excerpt from my ~/.intermine/simrmine.properties

db.production.datasource.serverName=localhost
db.production.datasource.port=5432
db.production.datasource.databaseName=simrmine
db.production.datasource.user=intermine
db.production.datasource.password=xxxxx

I have no problems when log into the simrmine database manually with psql with the user intermine and the password. I double checked the port, and it is 5432.

Thank you for your help!
Sofia



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Re: setting up chado (tripal) intermine

Julie Sullivan
Sorry Sofia I have no idea. Some systems administration problem?

Can you send me (off the list!) your entire properties file? I might be
able to spot a problem. Although the error message makes it clear the
properties are being parsed correctly.

Can you send me the entire error message?

Thanks!

On 09/12/14 14:37, Sofia Robb wrote:

> Hi Julie,
>
> I added the line
> "host all all 0.0.0.0/0 <http://0.0.0.0/0> password"
> to my pg_hba.conf file, stopped and restarted my postgres service and I
> still have this error:
>
>
> BUILD FAILED
> /data/src/intermine/imbuild/library.xml:78: The following error occurred
> while executing this line:
> /data/src/intermine/imbuild/objectstore.xml:93:
> java.lang.NullPointerException: Datasource is null. Properties are:
> {datasource.port=5432, datasource.user=intermine, platform=PostgreSQL,
> datasource.databaseName=simrmine, datasource.serverName=localhost,
> driver=org.postgresql.Driver, datasource.password=xxxxx,
> datasource.maxConnections=50}
>
> Thank you,
> Sofia
>
> On Mon, Dec 8, 2014 at 8:23 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Did you update the postgres pg_hba.conf file?
>
>     http://intermine.readthedocs.__org/en/latest/system-__requirements/software/__postgres/postgres/
>     <http://intermine.readthedocs.org/en/latest/system-requirements/software/postgres/postgres/>
>
>     ----
>
>
>     Hi Julie,
>     Thank you so much. I made the change and that error is gone, but now
>     I have another
>
>     BUILD FAILED
>     /data/src/intermine/imbuild/__library.xml:78: The following error
>     occurred while executing this line:
>     /data/src/intermine/imbuild/__objectstore.xml:93:
>     java.lang.__NullPointerException: Datasource is null. Properties
>     are: {datasource.port=5432, datasource.user=intermine,
>     platform=PostgreSQL, datasource.databaseName=__simrmine,
>     datasource.serverName=__localhost, driver=org.postgresql.Driver,
>     datasource.password=xxxx, datasource.maxConnections=50}
>
>     Here is the excerpt from my ~/.intermine/simrmine.__properties
>
>     db.production.datasource.__serverName=localhost
>     db.production.datasource.port=__5432
>     db.production.datasource.__databaseName=simrmine
>     db.production.datasource.user=__intermine
>     db.production.datasource.__password=xxxxx
>
>     I have no problems when log into the simrmine database manually with
>     psql with the user intermine and the password. I double checked the
>     port, and it is 5432.
>
>     Thank you for your help!
>     Sofia
>
>

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