Re: [Gusdev-gusdev] DoTS:NAEntry and topology

[Fidel S. <fi...@vb...>]

Angel,

I am not sure I totally understand your mail because I first want to
make sure you understand what I am trying to do.  What I want to do is
to add a column to a table before installing GUS.  That is, I want to
add a column to the SQL statement that creates the table 
(dots-tables.sql:CREATE TABLE DoTS.NAENTRY ().  From Chris's and your
previous answer nothing will break.  By nothing, I understand not the
installation and not the parsers. Correct?

Thanks

Fidel


Angel Pizarro <an...@pc...> writes:

     > BTW,
>
     > I did not mention this, but adding a column in the GUS system is not
     > completely trivial. Since the default columns are assumed to be at the
     > end of the column list, and adding a column in most RDBMSs appends to
     > the column list, you in fact have to create a new temporary table
     > where the added column precedes the "modification_date".
     > The added column is usually nullable and thus a select statement is
     > used to populate the temp table from the old:
>
     > insert into <new_table>  (<column list from old table>) select * from
     > <original_table>;
>
     > If the column is to be non-null, then you have to provide some default
     > value in the column listing of the select clause of the insert
     > statement:
>
     > insert into <new_table>  (<column list from NEW table>) select <non
     > default columns from old table>, <default_value>, <GUS default column
     > list>  from <original_table>;
>
     > Then you rename the old/new tables, drop and recreate the constraints
     > (the constraints will follow the old table as you rename, so if you
     > don't drop them first or you will have name clashes) and then the
     > object layer sees the new table definition. I'll release this as GUS
     > 3.1.1
>
     > Angel
     > Angel Pizarro wrote:
>
>> Adding the column will not break anythiing, although I ask you to
>> post a tracker item on the SF.net site. :
>>
>> http://sourceforge.net/tracker/?atid=479181&group_id=54213&func=browse
>>
>> Also, please attach the SQL to make that makes the new table,
>> transfers the data, apply constraints  and rename the tables
>> appropriately, etc., to the tracker item. Since you have to do these
>> actions regardless, it would be nice to share them as a script ;)
>>
>> I'll commit the change to CVS when I make the other changes that are
>> needed for GUS 3.1
>>
>> Angel
>>
>> Fidel Salas wrote:
>>
>>> Chris Stoeckert <sto...@pc...> writes:
>>>
>>>     > Hi Fidel,
>>>
>>> Hi Chris.  Thanks for your response.
>>>
>>>     > What are you trying to get from LOCUS?
>>>     > Here's an example for the kit gene (maybe you can send me a more
>>>     > relevant one for you).
>>>     > LOCUS NM_021099 5132 bp mRNA linear ROD 20-DEC-2003
>>>     > Is it the "linear" info?
>>>
>>> Yes, it is the "linear" (or "circular") info.
>>>
>>>     > I agree that NAEntry table would be a good place for this and
>>> I would
>>>     > recommend that the NAEntry table have a "topology" attribute
>>> added.
>>>     > I'm guessing that this information was lost because it's not
>>> something
>>>     > that we at CBIL use.
>>>
>>> Understood.
>>>
>>>     > My understanding is that nothing should should break by
>>> adding this
>>>     > column but would like others to confirm (Steve? Angel?)
>>>
>>> It sounds good.
>>>
>>> Fidel
>>>
>>>
>>>     > I also don't think that you would need to add set/get methods just
>>>     > alter the existing one for NAEntry.
>>>      > Chris
>>>      > On Jan 6, 2004, at 11:35 AM, Fidel Salas wrote:
>>>      > I need help in finding a quick solution to the following
>>> requirement.
>>>      > I need topology information for any given GenBank DNA
>>> sequence or
>>>     > entry.  This information is found in the LOCUS line of a GenBank
>>>     > entry.  For reasons unclear to me, the GBParser plugin parses
>>> this and
>>>     > then silently drops it.
>>>      > Since I am about to create a new GUS database, I would like
>>> to add a
>>>     > column to DoTS:NAEntry that will hold the topology
>>> information.  The
>>>     > main question is: will I break anything if I add this column
>>> to the
>>>     > tables sql script?
>>>      > Also, what is the reason this information is dropped?
>>>      > I am assuming getting GBParser to populate this new column
>>> would
>>>     > involve just getting the objrelp generator to add set and get
>>> methods.
>>>     > Is this all that would need to be done?
>>>      > Thanks
>>>      > Fidel
>>>
>>>>
>>>>
>>>>
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>>
>>
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