Re: [GUSDEV] ISF defaults

[<mro...@cs...>]

Steve,

The Core.TableInfo is also empty.

Since the installer did not load the default values,

at    http://www.gusdb.org/documentation/older/vbidoc.pdf

i looked in page 17 "Loading Data Into Gus" (i realize this is for versio=
n
3.0 but since we do not have a similar documentation for version 3.5) i
was wondering if i can follow those instructions to do "Initial
Population" of the tables they refer to, or is there any other place that
i can find the same information for the current version.


Thank you

Michael R


> 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, n=
ow
>>I assume that this value correspond to the field "name". Do I need to p=
ut
>>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 abo=
ut
>>>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 nam=
e
>>>"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 th=
e
>>>>following error:
>>>>
>>>>No row in Core.ProjectInfo has name =3D Database Administration'.  Th=
is
>>>>value was found in the project=3D 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=3DDatabase 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 th=
e
>>>>       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 an=
d
>>>>can
>>>>not continue until I find an answer.
>>>>
>>>>
>>>>Thank you
>>>>
>>>>
>>>>Michael Robinson
>>>>Bioinformatics Research Group (Biorg)
>>>>Florida International University
>>>>Miami, Florida, USA 33199
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>
>>
>>
>