Re: [GUSDEV] ISF defaults

[Steve F. <sfi...@pc...>]

i thought that the installer loaded default values into that table.

how about Core.TableInfo, is it filled?

yes, you do have to add the data you describe below

steve

mro...@cs... wrote:

>Steve,
>
>The Core.ProjectInfo table is empty, so I will create a record in
>
> project_id            | numeric(4,0)                | not null
> name                  | character varying(40)       | not null
> description           | character varying(255)      |
> release               | character varying(20)       |
> modification_date     | timestamp without time zone | not null
> user_read             | numeric(1,0)                | not null
> user_write            | numeric(1,0)                | not null
> group_read            | numeric(1,0)                | not null
> group_write           | numeric(1,0)                | not null
> other_read            | numeric(1,0)                | not null
> other_write           | numeric(1,0)                | not null
> row_user_id           | numeric(12,0)               | not null
> row_group_id          | numeric(4,0)                | not null
> row_project_id        | numeric(4,0)                | not null
> row_alg_invocation_id | numeric(12,0)               | not null
>Indexes:
>    "pk_projectinfo" primary key, btree (project_id)
>
>
>
>with the value "Database Administration" to match my gus.config file, now
>I assume that this value correspond to the field "name". Do I need to put
>any data in the other fields or is this up to me?
>
>Also before running ISF do I need to put any data in:
>
>        - SequenceOntology   (InsertSequenceOntology plugin)
>        - NCBI Taxon   (LoadTaxon plugin)
>        - External database and release (InsertExternalDatabase and
>                                  InsertExternalDatabaseRls plugins)
>        - at least one row in SequenceType so you can say what type of
>          sequence you are loading (you can use LoadRow plugin for this
>
>
>Thanks very much
>
>Michael R
>
>
>
>  
>
>>Michael-
>>
>>There is a table in gus called Core.ProjectInfo.  In contains info about
>>your "project."   When you run a plugin, the plugin needs to know what
>>the name of your project is so that all the rows you insert will be
>>assigned to your project.   The plugin discovers the name of your
>>project by looking in the gus.config file.
>>
>>The error message is telling you that the gus.config file is declaring
>>your project's name to be "Database Administration" while there is no
>>row in Core.ProjectInfo with name set to "Database Administration".
>>
>>Have you looked at the rows in that table?  Is there one with name
>>"Database Administration"?   On my GUS instance, I have a row with name
>>"Database administration"  (note the small 'a').   I suspect that this
>>row was put in by the gus installer.   So perhaps you just need to
>>change your config file to that.
>>
>>steve
>>
>>mro...@cs... wrote:
>>
>>    
>>
>>>Steve,
>>>
>>>I understand that you are in charge of ISF.
>>>
>>>I am trying to run the ISF plugin in a brand new install and I get the
>>>following error:
>>>
>>>No row in Core.ProjectInfo has name = Database Administration'.  This
>>>value was found in the project= property of your gus.config file.
>>>Please
>>>be sure it is correct and has been registered in the database
>>>**** GUS::PluginMgr::PluginError Failed running 'ga +meta --commit' with
>>>stderr:
>>>Operation now in progress**** GUS::PluginMgr::PluginError Failed
>>>running 'ga +update GUS::Supported::Plugin::InsertSequenceFeatures --
>>>commit' with stderr:
>>>
>>>I already checked my gus.config file and it has the entry
>>>
>>>project=Database Administration
>>>
>>>
>>>I would like to know if this and maybe other default values must be
>>>inserted into the database before trying to insert data.
>>>
>>>
>>>I found in the gusdev site the following:
>>>
>>>   From: Steve Fischer <sfischer@pc...> - 2005-08-31 10:32
>>>   for those of you who are using the beta version of the ISF plugin:
>>>   1. i will improve its documentation to indicate what it expects to
>>>      already be in the database:
>>>          - SequenceOntology   (InsertSequenceOntology plugin)
>>>          - NCBI Taxon   (LoadTaxon plugin)
>>>          - External database and release (InsertExternalDatabase and
>>>                                   InsertExternalDatabaseRls plugins)
>>>          - at least one row in SequenceType so you can say what type of
>>>            sequence you are loading (you can use LoadRow plugin for
>>>this)
>>>
>>>   2.  i will improve the error messages so that it better detects the
>>>       absence of these, and makes it more clear what to do.
>>>
>>>
>>>
>>>I am sorry if I ask the same question so many times but I am stuck and
>>>can
>>>not continue until I find an answer.
>>>
>>>
>>>Thank you
>>>
>>>
>>>Michael Robinson
>>>Bioinformatics Research Group (Biorg)
>>>Florida International University
>>>Miami, Florida, USA 33199
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>      
>>>
>
>  
>