gusdev-gusdev — Topics concerning GUS development

Re: [Gusdev-gusdev] Boolean query error

[Arnaud K. <ax...@sa...>]

That's all correct.

I haven't investigated further but I reckon the reference to the non-existent
cache table in an entry in the queries table (correct me if I'm wrong). So we
need a way to delete this entry or roll it back if it is possible.

Quoting Steve Fischer <st...@pc...>:

> if i understand paul correctly, then the problem is this:
>   1. query 1 produces SQLIdResultTable_1
>   2. query 2 times out, leaving as an artifact a broken 
> SQLIdResultTable, ie one without a valid cached result.
>   3. the boolean intersect operator tries to intersect these and bombs 
> out, producing an empty result?
>   4. is it also the case that if the user tries to redo query 2, outside 
> of the boolean context, then it again produces no result because it is 
> trying to reference the non-existent cache table?
> 
> steve
> 
> 
> Pjm wrote:
> 
> > Adrian Roy Tivey wrote:
> >
> >>> Arnaud-
> >>>
> >>> Jonathan has handed responsibility for the WDK over to me and Angel, 
> >>> since he has moved to D.C.
> >>>
> >>> I'll look into it.  Feel free to delve into the code and find out 
> >>> whatever you can.
> >>>
> >>> Steve
> >>
> >>
> >>
> >> Does anybody know how reliable Statement.setQueryTimeout is on 
> >> Oracle? If it's
> >> robust we could easily switch to that. Then we get the timeout report 
> >> in (more
> >> or less) the right bit of the code to handle it.
> >
> >
> > The statement timeout code works fine. Its more the fact that if one 
> > of the sub queries fails (for whatever reason) then the cacheXXXX 
> > table does not get created. Thus the query that intersects with it 
> > will also fail. The code does not handle this and the results page has 
> > a table with no rows.
> >
> > The next time that query runs it will look for the cacheXXXX table and 
> > fail. The user will think the query found nothing.
> >
> > Paul.
> >
> 

Re: [Gusdev-gusdev] Boolean query error

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

if i understand paul correctly, then the problem is this:
  1. query 1 produces SQLIdResultTable_1
  2. query 2 times out, leaving as an artifact a broken 
SQLIdResultTable, ie one without a valid cached result.
  3. the boolean intersect operator tries to intersect these and bombs 
out, producing an empty result?
  4. is it also the case that if the user tries to redo query 2, outside 
of the boolean context, then it again produces no result because it is 
trying to reference the non-existent cache table?

steve


Pjm wrote:

> Adrian Roy Tivey wrote:
>
>>> Arnaud-
>>>
>>> Jonathan has handed responsibility for the WDK over to me and Angel, 
>>> since he has moved to D.C.
>>>
>>> I'll look into it.  Feel free to delve into the code and find out 
>>> whatever you can.
>>>
>>> Steve
>>
>>
>>
>> Does anybody know how reliable Statement.setQueryTimeout is on 
>> Oracle? If it's
>> robust we could easily switch to that. Then we get the timeout report 
>> in (more
>> or less) the right bit of the code to handle it.
>
>
> The statement timeout code works fine. Its more the fact that if one 
> of the sub queries fails (for whatever reason) then the cacheXXXX 
> table does not get created. Thus the query that intersects with it 
> will also fail. The code does not handle this and the results page has 
> a table with no rows.
>
> The next time that query runs it will look for the cacheXXXX table and 
> fail. The user will think the query found nothing.
>
> Paul.
>

Re: [Gusdev-gusdev] Boolean query error

[Pjm <pj...@sa...>]

Adrian Roy Tivey wrote:
>>Arnaud-
>>
>>Jonathan has handed responsibility for the WDK over to me and Angel, 
>>since he has moved to D.C.
>>
>>I'll look into it.  Feel free to delve into the code and find out 
>>whatever you can.
>>
>>Steve
> 
> 
> Does anybody know how reliable Statement.setQueryTimeout is on Oracle? If it's
> robust we could easily switch to that. Then we get the timeout report in (more
> or less) the right bit of the code to handle it.

The statement timeout code works fine. Its more the fact that if one of the sub 
queries fails (for whatever reason) then the cacheXXXX table does not get 
created. Thus the query that intersects with it will also fail. The code does 
not handle this and the results page has a table with no rows.

The next time that query runs it will look for the cacheXXXX table and fail. 
The user will think the query found nothing.

Paul.

Re: [Gusdev-gusdev] Boolean query error

[Adrian R. T. <ar...@sa...>]

> Arnaud-
> 
> Jonathan has handed responsibility for the WDK over to me and Angel, 
> since he has moved to D.C.
> 
> I'll look into it.  Feel free to delve into the code and find out 
> whatever you can.
> 
> Steve

Does anybody know how reliable Statement.setQueryTimeout is on Oracle? If it's
robust we could easily switch to that. Then we get the timeout report in (more
or less) the right bit of the code to handle it.

Adrian 

> 
> Arnaud Kerhornou wrote:
> 
> >Hi Jonathan
> >
> >We've found an error with the boolean queries.
> >It happens when a query goes over timeout. The statement is reclaimed
> >(see code in reclaimLongRunningStatements() method of the Connection
> >class) and the cache table is not created.
> >But this cache table is expected to exist and we get a "table or view
> >does not exist" exception.
> >So every time someone is trying to do the same query again the code
> >tries to query the cache table and as a consequence, it doesn't return
> >any result.
> >
> >I don't know if I've made myself clear but I can give you the errput if
> >you want.
> >
> >Do you know how to fix this ? Would it be possible to insert a rollback
> >statement in the code when the statement is reclaimed ?
> >
> >cheers
> >Arnaud
> >

Re: [Gusdev-gusdev] Boolean query error

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

Arnaud-

let me try to better understand what you mean.

your subject line is 'boolean query error'.  is this problem limited to 
boolean queries?  i don't know exactly how they work, but i would guess 
that each query is run individually and then the set operations are 
applied to the results which reside in cache tables.  do you know if 
that is true?  if so, then the problem resolves down to how we handle 
timed out queries, ie, that we should expunge them from the table that 
points to the cached results.

steve

Arnaud Kerhornou wrote:

>Hi Jonathan
>
>We've found an error with the boolean queries.
>It happens when a query goes over timeout. The statement is reclaimed
>(see code in reclaimLongRunningStatements() method of the Connection
>class) and the cache table is not created.
>But this cache table is expected to exist and we get a "table or view
>does not exist" exception.
>So every time someone is trying to do the same query again the code
>tries to query the cache table and as a consequence, it doesn't return
>any result.
>
>I don't know if I've made myself clear but I can give you the errput if
>you want.
>
>Do you know how to fix this ? Would it be possible to insert a rollback
>statement in the code when the statement is reclaimed ?
>
>cheers
>Arnaud
>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] Boolean query error

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

Arnaud-

Jonathan has handed responsibility for the WDK over to me and Angel, 
since he has moved to D.C.

I'll look into it.  Feel free to delve into the code and find out 
whatever you can.

Steve

Arnaud Kerhornou wrote:

>Hi Jonathan
>
>We've found an error with the boolean queries.
>It happens when a query goes over timeout. The statement is reclaimed
>(see code in reclaimLongRunningStatements() method of the Connection
>class) and the cache table is not created.
>But this cache table is expected to exist and we get a "table or view
>does not exist" exception.
>So every time someone is trying to do the same query again the code
>tries to query the cache table and as a consequence, it doesn't return
>any result.
>
>I don't know if I've made myself clear but I can give you the errput if
>you want.
>
>Do you know how to fix this ? Would it be possible to insert a rollback
>statement in the code when the statement is reclaimed ?
>
>cheers
>Arnaud
>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

[Gusdev-gusdev] Boolean query error

[Arnaud K. <ax...@sa...>]

Hi Jonathan

We've found an error with the boolean queries.
It happens when a query goes over timeout. The statement is reclaimed
(see code in reclaimLongRunningStatements() method of the Connection
class) and the cache table is not created.
But this cache table is expected to exist and we get a "table or view
does not exist" exception.
So every time someone is trying to do the same query again the code
tries to query the cache table and as a consequence, it doesn't return
any result.

I don't know if I've made myself clear but I can give you the errput if
you want.

Do you know how to fix this ? Would it be possible to insert a rollback
statement in the code when the statement is reclaimed ?

cheers
Arnaud

[Gusdev-gusdev] JavaServer Faces

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

in his poking around learning about JSF, Angel came across this article.

i have read a bit of it, and it seems to anwer definitively that JSF and 
Tiles are complimentary. JSF is roughly like Swing.

http://www-106.ibm.com/developerworks/library/j-integrate/?ca=dnt-438

steve

Re: [Gusdev-gusdev] Permissions for running ga

[Jonathan C. <cra...@pc...>]

Hi Han-

Han Sang Rhee wrote:
> Hello,
> 
> I am a new gus user and am having some difficulties figuring some things 
> out.
> 
> I would like to know what the minimum OS level permissions are needed for 
> running "ga".  I seem to only beable to run it as root or my oracle user.  
> I get the following error message when I try to run it as anybody else:
> 
> RAD' --group 'dba' --user 'three' --commit
> Reading properties from /opt/gus_home/config/GUS-PluginMgr.prop
> Reading properties from /opt/.gus.properties
> install_driver(Oracle) failed: Can't load 
> '/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/auto/DBD/Oracle/Oracle.so' 
> for module DBD::Oracle: libclntsh.so.9.0: cannot open shared object file: 

It looks like the Perl module DBD::Oracle is unable to access one of the
Oracle client libraries.  This could be due to the permissions on the file
(libclntsh.so.9.0) being set incorrectly, but is more likely because the
directory that contains this file is not in your "LD_LIBRARY_PATH" Unix
environment variable.  I would recommend taking the following steps:

1. Check that the directory $ORACLE_HOME/lib appears in the LD_LIBRARY_PATH
   environment variable of the user that's trying to run 'ga'.  The value of
   $ORACLE_HOME must also be set, of course, and its location will depend on
   where Oracle is installed on your machine.
2. If ga still does not work, look at the files in $ORACLE_HOME/lib and
   make sure that libclntsh.so.9.0 exists and is readable by the user that's
   trying to run 'ga'.

You can also just compare the environment variable settings for $ORACLE_HOME
and $LD_LIBRARY_PATH between a user that can run 'ga' successfully and one
that cannot.  Regards,

Jonathan

[Gusdev-gusdev] Permissions for running ga

[Han S. R. <rh...@dr...>]

Hello,

I am a new gus user and am having some difficulties figuring some things 
out.

I would like to know what the minimum OS level permissions are needed for 
running "ga".  I seem to only beable to run it as root or my oracle user.  
I get the following error message when I try to run it as anybody else:

RAD' --group 'dba' --user 'three' --commit
Reading properties from /opt/gus_home/config/GUS-PluginMgr.prop
Reading properties from /opt/.gus.properties
install_driver(Oracle) failed: Can't load 
'/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi/auto/DBD/Oracle/Oracle.so' 
for module DBD::Oracle: libclntsh.so.9.0: cannot open shared object file: 
No such file or directory at 
/usr/lib/perl5/5.8.0/i386-linux-thread-multi/DynaLoader.pm line 229.
 at (eval 4) line 3
Compilation failed in require at (eval 4) line 3.
Perhaps a required shared library or dll isn't installed where expected
 at /opt/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 152

I'm running Oracle 9.2 on Redhat Linux 8.0 

Any help would be greatly appreciated.

-Han

Re: [Gusdev-gusdev] how can I search post?

[Terry C. <tw...@cs...>]

Hi Sam,
The db document is a plain text one that might not
be posted. I think Jessica's group is tuned into this 
list and will get back to you. 

Terry


On  0, sam wang <gus...@ya...> wrote:
> Dear friends,
>  
> from the post made by Terry Clark, I know there is a post made by  Jessica Kissinger about the configuration of GUS database. the problem is that I can't find this post using search function provided by this maillist website.
>  
> would you please let me know where is the post and how can I use the search function in this maillist website if you have any idea.
>  
> thank you very much!
>  
> Sincerely yours,
> Sam wang
> 
> 
> ---------------------------------
> Do you Yahoo!?
> Yahoo! SiteBuilder - Free, easy-to-use web site design software

[Gusdev-gusdev] how can I search post?

[sam w. <gus...@ya...>]

Dear friends,
 
from the post made by Terry Clark, I know there is a post made by  Jessica Kissinger about the configuration of GUS database. the problem is that I can't find this post using search function provided by this maillist website.
 
would you please let me know where is the post and how can I use the search function in this maillist website if you have any idea.
 
thank you very much!
 
Sincerely yours,
Sam wang


---------------------------------
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software

[Gusdev-gusdev] cvsmod: helpful little tool

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

folks-

i have a teeny little tool which helps us keep our cvs repository well 
commented.

one of the big problems in documenting your changes in cvs is this:  you 
have been working on a few things that are not really related.  and now 
you want to check in your stuff.  the easiest way is:
   %cd $PROJECT_HOME/GUS      #eg, go to the root of your module
   %cvs commit -m "some comment here, or... worse, none at all"

The problem is that you are commenting ALL the files you have changed, 
but they aren't all related.

An alternative approach, and probably the best, is to use emac's version 
control tools to check in your files individually, as soon as you make 
changes.  however, that doesn't work if you are hitting a bunch of files 
and are in a develop/debug loop.

So, i use cvsmod.

All it does is give you a report of the files that you have changed:

[sfischer@pythia GUS]$ cvsmod
File: DialogFactoryPlasmoDB.java        Status: Locally Modified
File: QueryHistoryPage.java     Status: Locally Modified
File: QueryPage.java    Status: Locally Modified
File: SQLIdResultTable.java     Status: Locally Modified
File: reportMaker.pl.in Status: Locally Modified
File: rnaSimilarityPng.pm.in    Status: Locally Modified

Then, you can do individualized check-ins for one or more of those 
files, giving them the proper comment.

When you are all done, cvsmod will not return any files that have been 
modified.

And, the best part is that cvsmod is utterly trivial.  Here it is:

#!/bin/csh
cvs status |& grep Modified

I have put it into my local bin.  If you are at CBIL,you can copy it from:
/home/sfischer/mybin/cvsmod

Steve



  

[Gusdev-gusdev] new plugin

[Elisabetta M. <man...@pc...>]

Hi all,
I've written a new plugin to populate the (new) RAD3 tables for analysis 
results. It's a generic plugin which can be used with any view of 
AnalysisResultImp.

You can find it in the Sanger cvs repository:

GUS/RAD/plugin/perl/AnalysisResultLoader.pm

The documentation is also available from cvs
(GUS/RAD/doc/AnalysisResultLoader.html) 

Elisabetta
--
Elisabetta Manduchi

Computational Biology and Informatics Laboratory
Center for Bioinformatics
University of Pennsylvania
1428 Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104-6021

phone: 215-573-4408
fax: 215 573-3111
email: man...@pc...
web: http://www.cbil.upenn.edu/~manduchi

---

[Gusdev-gusdev] modificaton to Plugin.pm

[Elisabetta M. <man...@pc...>]

I've cvs committed a change to GUS/PluginMgr/lib/perl/Plugin.pm, suggested 
by Steve, to fix a problem occurring when registering a new plugin written 
using the most recent documentation features.
Elisabetta

Re: [Gusdev-gusdev] can I install GUS on linux Redhat 9.0?

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

yes, you can use redhat 9.0.  

I hope soon to post GUS install instructions created by Terry Clark.

Steve

sam wang wrote:

> Dear friends,
>  
> can I install GUS on linux Redhat 9.0 if I install GUS project based 
> on JSP/Servlet? I heard Redhat 9.0 is really nice comparing with the 
> old linux version. and does there any difference with the old linux 
> version? I mean does there any special procedure or configuration 
> about the linux 9?
>  
> also I read an thread authored by Jessica Kissinger, in the thread, 
> you said: p.s. We have documented what we have learned, it will get 
> easier.
> so I wonder if you can send this document to me. it will be definitely 
> helpful to me! thank you so much for the great help in advance. my 
> mailbox is: gus...@ya... <mailto:gus...@ya...>
>  
> or does there any such kind of installation document describing the 
> installation in details. I definitely need them!   :-)
>  
> thank you all!
>  
> best wishes,
> Sammy
> ------------------------------------------------------------------------
> Do you Yahoo!?
> Yahoo! SiteBuilder 
> <http://us.rd.yahoo.com/evt=10469/*http://sitebuilder.yahoo.com> - 
> Free, easy-to-use web site design software 

[Gusdev-gusdev] can I install GUS on linux Redhat 9.0?

[sam w. <gus...@ya...>]

Dear friends,
 
can I install GUS on linux Redhat 9.0 if I install GUS project based on JSP/Servlet? I heard Redhat 9.0 is really nice comparing with the old linux version. and does there any difference with the old linux version? I mean does there any special procedure or configuration about the linux 9?
 
also I read an thread authored by Jessica Kissinger, in the thread, you said: p.s. We have documented what we have learned, it will get easier.
so I wonder if you can send this document to me. it will be definitely helpful to me! thank you so much for the great help in advance. my mailbox is: gus...@ya...
 
or does there any such kind of installation document describing the installation in details. I definitely need them!   :-)
 
thank you all!
 
best wishes,
Sammy


---------------------------------
Do you Yahoo!?
Yahoo! SiteBuilder - Free, easy-to-use web site design software

[Gusdev-gusdev] GUS WDK architecture meeting summary

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

Folks-

We had an informal first technical meeting of possible core developers 
of the next generation GUS WDK.  The goal was to set some architectural 
foundations and get oriented.  We covered the part of the WDK that 
specifies web sites.  We did not cover web services, which is likely to 
be largely independent of this part of the WDK.

As this was a technical meeting, we did not cover scheduling or human 
resources issues.

Included in the meeting were
  Adrian
  Arnaud
  Angel
  Dave
  Jonathan S.
  Steve

We converged on a number of ideas:
  1. use struts/jsp
  2. continue using a configurable JavaBeans based model
  3. the model will be similar to the current WDK's model.
  4. however, its configuration file(s) will not include any view 
configuration, as does the current WDK config file
  5. the view will rely heavily on custom tags to provide renderers for 
the data types found in the model
  6. we need to figure out how to aggregate custom tags to provide 
 higher level re-usable view elements.  we might use tiles for this.
  7. we will look into JavaServlet Faces to see how it can help us 
organize our view design.
  8. at the outset, we will author JSP pages to provide the framework 
for the view.  in particular, we expect to start with dedicated pages 
for top-level records such as Gene, RNA, giving these pages a hand 
edited look.  These will call out to the tags or tag aggregates.   We 
will ultimately evaluate whether that kind of hand authoring is becoming 
unscalable.  If so, we will add a facility to generate those kind of 
pages from the model, allowing for minimal configuration as needed.  We 
call this facility the rendering engine.
  9. As with the current WDK, the model includes the queries that are 
available to the users. [I am proposing that this part of the model 
could be called the Questions model.  The other part of the model has 
Answers, such as Records and ResultSets.  The model will also include 
ComplexQuestions.  I am steering away from the word "query" because it 
is over-used in this context (Answers use queries to format themselves).]
 10. a good way to get rolling is to produce a UML spec. for the 
Questions model, and then to make a view.
 11. we expect to rely on struts for stuff like logging, error handling, 
connection pooling and possible process pooling
 12. we expect to continue to use our own sophisticated facility for 
Question parameter validation (a la CSP) rather than struts's validation

The action items were:
  1. angel: give a report on JavaServlet Faces
  2. adrian: give a report on the usefulness of tiles given our expected 
use of custom tags
  3. adrian: put together a UML spec. for the Questions model

Steve

Re: [Gusdev-gusdev] batch submission demo

[<su...@vb...>]

Hi,

I have a question. If GUS has any scripts for pipelining the genomic shut
gun data to assemblies and storing them into the database.

Sucheta
> folks-
>
> i have a prototype of the batch submission interface for you to try out.
>  This is the idea that our web based queries will be able to take a list
> of values instead of just one (eg, locus link ids) or provide a file
> with the list.  This is a feature of our WDK, and so will be available
> to all web projects.
>
> here is the link:
>
> https://www.cbil.upenn.edu/dotsgenes-dev/servlet/servlet?page=query&showForm=1&query=datasetTest
>
> Its on the dotsgenes-dev site.
>
> logn: cbil
> pword:  Ep79dots (this is not a high-security password, just one to ward
> the public away from our work in progress)
>
> here are the highlights:
>   - you should be able to provide a dataset  (btw, 1111 and 2222 are
> locuslinks that we map to)
>   - you should get a set of DTs as result
>   - you can go to history and see your result there
>   - you can go to download from history to get a ReportMaker report
>   - you can click on the column which has your input data set to include
> it in the report
>   - you can also run other queries.  if they show up in the history, you
> can ask to download them, and will have the option of choosing any
> datasets you have input as a column in the report
>
> please find bugs...
>
> and PLEASE comment on the query dialog page.  will our users understand
> what they have to do there?  if not, how should i improve it?
>
> steve
>
>
>
> -------------------------------------------------------
> This sf.net email is sponsored by:ThinkGeek
> Welcome to geek heaven.
> http://thinkgeek.com/sf
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>


-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138

[Gusdev-gusdev] future ideas for WDK

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

folks-

just wanted to throw out there a couple of ideas that jonathan schug and 
i batted around yesterday for future features of the GUS Web Development 
Kit (WDK).

1. History mode offers the ability to adjust and re-do the query 
(including complex queries).  IE, offers a link that dumps the user into 
the boolean query page initialized with the values from the history 
query, including the union, intersections, etc.  The user can tweek the 
values and re-run the query.

2. An extention of the shopping cart idea that Schug has been thinking 
about:  any result set page (eg, a list of transcripts or experiments) 
allows the user to select individual elements from the set and put them 
into a "shopping cart".  There is a default shopping cart for each type 
of entity.  Furthermore, the user can give a shopping cart a name, and 
choose which one is the default.  IE, the user can have named sets of 
entities that they hand picked.  They will also show up in the history.

steve

[Gusdev-gusdev] batch submission demo

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

folks-

i have a prototype of the batch submission interface for you to try out. 
 This is the idea that our web based queries will be able to take a list 
of values instead of just one (eg, locus link ids) or provide a file 
with the list.  This is a feature of our WDK, and so will be available 
to all web projects.

here is the link:

https://www.cbil.upenn.edu/dotsgenes-dev/servlet/servlet?page=query&showForm=1&query=datasetTest

Its on the dotsgenes-dev site.

logn: cbil
pword:  Ep79dots (this is not a high-security password, just one to ward 
the public away from our work in progress)

here are the highlights:
  - you should be able to provide a dataset  (btw, 1111 and 2222 are 
locuslinks that we map to)
  - you should get a set of DTs as result
  - you can go to history and see your result there
  - you can go to download from history to get a ReportMaker report
  - you can click on the column which has your input data set to include 
it in the report
  - you can also run other queries.  if they show up in the history, you 
can ask to download them, and will have the option of choosing any 
datasets you have input as a column in the report

please find bugs...

and PLEASE comment on the query dialog page.  will our users understand 
what they have to do there?  if not, how should i improve it?

steve

Re: [Gusdev-gusdev] Struts documentation - supporting evidence

[Jonathan C. <cra...@pc...>]

Hi Sucheta-

On Thu, 4 Sep 2003 su...@vb... wrote:
> I am new to the GUS developer's forum, so I am not aware if the question
> has already been addressed.
> 
> I was wondering in the table DoTS::NAFeatureImp (standard table), what are
> the use of the int(1...), float(1..) and string attributes.
> 
> Is there a place where the meaning of the attributes has been documented?

As Chetna mentioned, documentation is available for many of the attributes 
in the GUS schema browser; see http://www.gusdb.org/cgi-bin/schemaBrowser
The descriptions that you see in the schema browser are actually stored in 
GUS itself, in the table Core.DatabaseDocumentation.

However, the particular attributes that you mention are handled in a 
special way.  Any table whose name ends in "Imp" in GUS is considered an 
"implementation" table.  These tables are typically not queried directly; 
instead we query the single-table views that are defined on these tables.  
In the case of NAFeatureImp, for example, these views include GeneFeature 
and HexamerFeature; the schema browser's "view on" column shows us that 
both of these views are views on the NAFeatureImp table.  The columns 
named int1, string1, etc., may be used for different things in different 
views, so the important thing to look at is the documentation for the 
individual views, not the implementation tables.  For example, if you 
click on the link for DoTS::GeneFeature, you can see the actual SQL view 
definition for the view, which reads as follows:

SELECT na_feature_id,
na_sequence_id,
subclass_view,
sequence_ontology_id,
name,
parent_id,
source_id,
external_database_release_id,
prediction_algorithm_id,
is_predicted,
review_status_id,
string14 as gene_type,
tinyint2 as confirmed_by_similarity,
int1 as prediction_number,
int2 as number_of_exons,
tinyint3 as has_initial_exon,
tinyint4 as has_final_exon,
float1 as score,
float2 as secondary_score,
tinyint5 as is_pseudo,
tinyint6 as is_partial,
string1 as allele,
string2 as citation,
string3 as evidence,
string4 as function,
string5 as gene,
string6 as label,
string7 as map,
string9 as phenotype,
string10 as product,
string12 as standard_name,
string13 as usedin,
modification_date,
user_read,
user_write,
group_read,
group_write,
other_read,
other_write,
row_user_id,
row_group_id,
row_project_id,
row_alg_invocation_id,
FROM NAFeatureImp WHERE subclass_view = 'GeneFeature' WITH CHECK OPTION;

In other words, the "string1" column of the NAFeatureImp table is used to 
store the GeneFeature's "allele".  But, in another view of NAFeatureImp, 
it might be used for something else.  This system of having multiple views 
on a single implementation table gives us a very simple way to implement a 
restricted form of subclassing in the database (that is, a GeneFeature 
IS-A NAFeature.)

Jonathan

[Gusdev-gusdev] Understanding Imp tables

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

[I have re-subjected this email thread]

The table you are looking at is an "Imp" table.  These are special 
tables that are used by GUS to implement subclassing.

GUS allows us to define a single level subclass structure.  For example, 
we can define NAFeature as a base class, and, eg, GeneFeature and 
ExonFeature as subclasses of NAFeature.  

This is done by a trick.  The subclasses are views of an Imp table which 
really holds the data.  The "Imp" stands for implementation.  In a 
sense, you should consider these tables as hidden.  In this case, the 
base class view is NAFeature.  Its implementation table is NAFeatureImp. 
 And the subclass views are GeneFeature, etc.  The columns in an Imp 
table are just named for the kind of data they hold, and are never 
expected to be accessed directly.  Instead you use the views, either the 
base class (NAFeature) or the subclasses (GeneFeature).

steve

Chetna Warade wrote:

>Hello Sucheta,
>
>I dont know if this is what you looking for but checkout 
>http://www.gusdb.org/cgi-bin/schemaBrowser and scroll for
>DOTS::Tablename you should ab able to find the table
>decription. Most of the times the table field names are
>intuitative.
>
>Chetna
>
>---- Original message ----
>  
>
>>Date: Thu, 4 Sep 2003 12:56:47 -0400 (EDT)
>>From: su...@vb...  
>>Subject: Re: [Gusdev-gusdev] Struts documentation -
>>    
>>
>supporting evidence  
>  
>
>>To: "Steve Fischer" <sfi...@pc...>
>>Cc: "Adrian Roy Tivey" <ar...@sa...>,
>>    
>>
>gus...@li...
>  
>
>>Hi,
>>I am new to the GUS developer's forum, so I am not aware if
>>    
>>
>the question
>  
>
>>has already been addressed.
>>
>>I was wondering in the table DoTS::NAFeatureImp (standard
>>    
>>
>table), what are
>  
>
>>the use of the int(1...), float(1..) and string attributes.
>>
>>Is there a place where the meaning of the attributes has been
>>    
>>
>documented?
>  
>
>>Sucheta
>>
>>    
>>
>>>Adrian, see below.
>>>
>>>steve
>>>
>>>Adrian Roy Tivey wrote:
>>>
>>>      
>>>
>>>>Hello,
>>>>
>>>>Thanks for your comments. Just a shortish email to expand
>>>>        
>>>>
>on a couple of
>  
>
>>>>points and request clarification on a couple of others
>>>>        
>>>>
>(including
>  
>
>>>>comments on
>>>>the first three points but that's just the order they
>>>>        
>>>>
>happened to come
>  
>
>>>>up!)
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>>Adrian-
>>>>>
>>>>>Angel and I have had a chance to meet and throw together
>>>>>          
>>>>>
>our initial
>  
>
>>>>>ideas about a JSP/Struts based WDK.
>>>>>
>>>>>My sense is that our thinking compliments what you layed
>>>>>          
>>>>>
>out in your
>  
>
>>>>>Struts Demo.  Basically, we are buying into the ideas you
>>>>>          
>>>>>
>presented
>  
>
>>>>>about how the display can work.  We are also interested in
>>>>>          
>>>>>
>starting to
>  
>
>>>>>nail down the design of the underlying machinery (somewhat
>>>>>          
>>>>>
>along the
>  
>
>>>>>lines of what you outlined in your conclusions section). 
>>>>>          
>>>>>
>Much of our
>  
>
>>>>>thinking is informed by the current WDK design.
>>>>>
>>>>>We drew up a quick list of big-ticket requirements items,
>>>>>          
>>>>>
>some addressed
>  
>
>>>>>by your proposal and some not:
>>>>> - declarative specification of content, queries, dialogs.
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>I follow the middle one. I'm not sure what you mean by
>>>>        
>>>>
>dialog and
>  
>
>>>>especially
>>>>content through the email. Could you give a rough outline
>>>>        
>>>>
>of the Content
>  
>
>>>>bean?
>>>>
>>>>
>>>>        
>>>>
>>>By "content" we mean all kinds of verbiage on the site. 
>>>      
>>>
>The canonical
>  
>
>>>example is the tutorials available on the EpconDB site
>>>(http://www.cbil.upenn.edu/EPConDB/).  The content is
>>>      
>>>
>considered "model"
>  
>
>>>not view.   The current implementation is Jonathan Schug's Page
>>>Generator, which is written in perl.  The model is stored
>>>      
>>>
>in perl data
>  
>
>>>structures, independently from any formatting information,
>>>      
>>>
>and is
>  
>
>>>formated by the PageGenerator.  Its not always obvious
>>>      
>>>
>where to draw the
>  
>
>>>line between model and view.  Another example would be that
>>>      
>>>
>a home page
>  
>
>>>might have Introduction, News, Funding, etc. that we would
>>>      
>>>
>like to be in
>  
>
>>>the model.  Obviously, in the new WDK, model is stored in
>>>      
>>>
>Beans, and
>  
>
>>>view is stored mostly in JSP.
>>>
>>>By "dialog" we mean a form.  In the current WDK, the
>>>      
>>>
>dialogues are
>  
>
>>>specified declaratively in the servlet-config file.  They
>>>      
>>>
>are often
>  
>
>>>complex, with queries underlying pulldown lists, etc.  In
>>>      
>>>
>the new WDK we
>  
>
>>>were thinking we would have Dialog beans, or similar, to
>>>      
>>>
>manage these in
>  
>
>>>the model.
>>>
>>>      
>>>
>>>>        
>>>>
>>>>> - configurable styles
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>ie given an query syntax tree the way this is displayed to
>>>>        
>>>>
>the user
>  
>
>>>>should be
>>>>easily modifiable, or something else?
>>>>
>>>>        
>>>>
>>>Bear with me here.  I still haven't read the JSP book yet.
>>>      
>>>
> But, the idea
>  
>
>>>is for the JSPs to refer to a stylesheet or similar, so
>>>      
>>>
>that we could
>  
>
>>>potentially reuse JSPs across projects.   An example would
>>>      
>>>
>be a JSP that
>  
>
>>>formats a query dialog.  The JSP is the same between, say,
>>>      
>>>
>allgenes and
>  
>
>>>plasmodb, but the look is different because of the style
>>>      
>>>
>configuration.  i
>  
>
>>>am not clear on how this relates to the tiles.
>>>
>>>      
>>>
>>>>        
>>>>
>>>>> - site's standard s surrounding page specific stuff (ie,
>>>>>          
>>>>>
>your tiles
>  
>
>>>>>solution)
>>>>> - JavaScript functionality
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Server-side scripting or client side?
>>>>
>>>>
>>>>        
>>>>
>>>client side.  we use this for example to provide mouse-over
>>>      
>>>
>behaviour in
>  
>
>>>some of our graphics.
>>>
>>>      
>>>
>>>>        
>>>>
>>>>> - calls to external resources (eg, processes) to provide
>>>>>          
>>>>>
>stuff like
>  
>
>>>>>graphics
>>>>> - boolean queries
>>>>> - history
>>>>> - report maker
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Is there a current implementation in one of the current GUS
>>>>        
>>>>
>sites or a
>  
>
>>>>spec
>>>>somewhere? It's been mentioned at this end but I don't
>>>>        
>>>>
>think we ever went
>  
>
>>>>into
>>>>it in much detail.
>>>>
>>>>        
>>>>
>>>I guess you are refering to the ReportMaker.  It is alive
>>>      
>>>
>on the
>  
>
>>>Allgenes site.  Do a query, and then press Download from
>>>      
>>>
>the query
>  
>
>>>history.  The code is in two places.  The backend is in cvs
>>>GUS/ReportMaker.  The frontend is still in our legacy CVS.
>>>
>>>      
>>>
>>>>
>>>>        
>>>>
>>>>> - batch submission
>>>>> - connection pooling
>>>>> - process pooling?
>>>>> - result caching
>>>>> - result paging
>>>>> - error handling
>>>>> - dialog validation
>>>>> - logging
>>>>>
>>>>>We sketched the following top level Beans, which we see
>>>>>          
>>>>>
>being configured
>  
>
>>>>>in config files (XML is fine... not sure yet about Digester)
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>I only suggested that because that's what's used by Struts.
>>>>        
>>>>
>Played with
>  
>
>>>>it a
>>>>bit more now and it seems simple to use for what we'd
>>>>        
>>>>
>want. But yes,
>  
>
>>>>there's
>>>>any number of mature, open-source XML/Beans alternatives we
>>>>        
>>>>
>could go for
>  
>
>>>>instead.
>>>>
>>>>
>>>>        
>>>>
>>>Angel has looked at Digester and got the sense that it was
>>>      
>>>
>overkill.  i
>  
>
>>>haven't looked at it yet.  we remain open-minded.
>>>
>>>      
>>>
>>>>>, and which
>>>>>do not specify any formatting information:
>>>>> - Dialog  (eg, a form)
>>>>> - QueryDialog (a subclass of Dialog)
>>>>> - other subclasses of Dialog?
>>>>> - Record (eg, an RNA page and/or detailed page)
>>>>> - ResultSet (or is this just a record?)
>>>>>
>>>>>These guys have properties, which, are also beans, of types:
>>>>> - Content
>>>>> - SqlQuery
>>>>> - Process
>>>>>
>>>>>And, SqlQuery and Process have as properties subclasses of
>>>>>          
>>>>>
>Param, which
>  
>
>>>>>is also a bean.
>>>>>
>>>>>The main difference between the beans we see for the new
>>>>>          
>>>>>
>WDK and those
>  
>
>>>>>in the old WDK is that the new ones don't include any
>>>>>          
>>>>>
>formatting
>  
>
>>>>>information.  I think that means that we can have
>>>>>          
>>>>>
>siginificantly fewer
>  
>
>>>>>classes, because the classes don't have to differentiate
>>>>>          
>>>>>
>based on
>  
>
>>>>>formatting implementations.
>>>>>
>>>>>Based on our still rudimentary understanding of JSP, we
>>>>>          
>>>>>
>imagine these
>  
>
>>>>>kind of pages and fragments, which are somehow
>>>>>          
>>>>>
>parameterized by the
>  
>
>>>>>beans:
>>>>>  - Dialog
>>>>>  - QueryDialog
>>>>>  - ResultSet
>>>>>  - Record
>>>>>  - Record Details
>>>>>  - Content
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>I suspect we may be thinking of two different things but
>>>>        
>>>>
>not sure. What
>  
>
>>>>kind of
>>>>thing would content be as a page or page fragment wrt a
>>>>        
>>>>
>Content bean?
>  
>
>>>>
>>>>        
>>>>
>>>A Content fragment would be a JSP fragment that could show
>>>      
>>>
>news items.
>  
>
>>>>        
>>>>
>>>>>Things we are assuming JSP can do (haven't read the book
>>>>>          
>>>>>
>yet), and want
>  
>
>>>>>to understand more about:
>>>>> - bind beans to a JSP page
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Yep. jsp:useBean to tie a JavaBean to a page local
>>>>        
>>>>
>variable. We have to
>  
>
>>>>decide
>>>>on a schedule and how cutting-edge we want to be. The
>>>>        
>>>>
>syntax becomes even
>  
>
>>>>clearer with JSP2.0 (eg Tomcat 5) but support for that is
>>>>        
>>>>
>still at
>  
>
>>>>alpha/beta
>>>>for many containers. (There *should* be a stable
>>>>        
>>>>
>implementation in
>  
>
>>>>~December for
>>>>the official release of J2EE 1.4 so personally I don't
>>>>        
>>>>
>think it's
>  
>
>>>>unreasonable
>>>>choice)
>>>>
>>>>
>>>>        
>>>>
>>>ok, lets keep that in mind.
>>>
>>>      
>>>
>>>>        
>>>>
>>>>> - simple control features like iterate across a list of
>>>>>          
>>>>>
>results to
>  
>
>>>>>display
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Not part of JSP per se but there is a standard template
>>>>        
>>>>
>library that
>  
>
>>>>includes
>>>>simple iterators, control flow etc. See
>>>>        
>>>>
>geneResults-body.jspf for an
>  
>
>>>>example
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>> - fetch JSP fragments to insert (eg, one per row of a
>>>>>          
>>>>>
>result)
>  
>
>>>>>          
>>>>>
>>>>? Not sure I understand. There are two built-in include
>>>>        
>>>>
>mechanisms but
>  
>
>>>>for a
>>>>table of results you'd generally write the formatting code
>>>>        
>>>>
>eg table tags
>  
>
>>>>as a
>>>>template and insert the data into that. For the specific
>>>>        
>>>>
>case of the
>  
>
>>>>CellFormatter there is a working tag library equivalent in
>>>>        
>>>>
>the demo.
>  
>
>>>>
>>>>        
>>>>
>>>>>As far as the config files are concerned, we agree that
>>>>>          
>>>>>
>huge config
>  
>
>>>>>files are not optimal.  We don't yet see how best to
>>>>>          
>>>>>
>organize them,
>  
>
>>>>>though we want to be able to re-use some of them across
>>>>>          
>>>>>
>projects.  So, i
>  
>
>>>>>think they will need to find there way into a directory
>>>>>          
>>>>>
>structure of
>  
>
>>>>>some kind.
>>>>>
>>>>>Steveo
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>Adrian
>>>>
>>>>
>>>>        
>>>>
>>>
>>>-------------------------------------------------------
>>>This SF.net email is sponsored by: VM Ware
>>>With VMware you can run multiple operating systems on a
>>>      
>>>
>single machine.
>  
>
>>>WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual
>>>      
>>>
>machines
>  
>
>>>at the same time. Free trial click
>>>here:http://www.vmware.com/wl/offer/358/0
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>      
>>>
>>-- 
>>Sucheta Tripathy
>>Virginia Bioinformatics Institute
>>1880 pratt drive,Bldg XV
>>Virginia tech.
>>Blacksburg
>>Virginia
>>VA 24061
>>phone-(540)231-8138
>>
>>
>>-------------------------------------------------------
>>This sf.net email is sponsored by:ThinkGeek
>>Welcome to geek heaven.
>>http://thinkgeek.com/sf
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>    
>>
>
>
>-------------------------------------------------------
>This sf.net email is sponsored by:ThinkGeek
>Welcome to geek heaven.
>http://thinkgeek.com/sf
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>  
>

Re: [Gusdev-gusdev] Struts documentation - supporting evidence

[Chetna W. <ch...@ug...>]

Hello Sucheta,

I dont know if this is what you looking for but checkout 
http://www.gusdb.org/cgi-bin/schemaBrowser and scroll for
DOTS::Tablename you should ab able to find the table
decription. Most of the times the table field names are
intuitative.

Chetna

---- Original message ----
>Date: Thu, 4 Sep 2003 12:56:47 -0400 (EDT)
>From: su...@vb...  
>Subject: Re: [Gusdev-gusdev] Struts documentation -
supporting evidence  
>To: "Steve Fischer" <sfi...@pc...>
>Cc: "Adrian Roy Tivey" <ar...@sa...>,
gus...@li...
>
>Hi,
>I am new to the GUS developer's forum, so I am not aware if
the question
>has already been addressed.
>
>I was wondering in the table DoTS::NAFeatureImp (standard
table), what are
>the use of the int(1...), float(1..) and string attributes.
>
>Is there a place where the meaning of the attributes has been
documented?
>
>
>Sucheta
>
>> Adrian, see below.
>>
>> steve
>>
>> Adrian Roy Tivey wrote:
>>
>>>Hello,
>>>
>>>Thanks for your comments. Just a shortish email to expand
on a couple of
>>>points and request clarification on a couple of others
(including
>>> comments on
>>>the first three points but that's just the order they
happened to come
>>> up!)
>>>
>>>
>>>
>>>>Adrian-
>>>>
>>>>Angel and I have had a chance to meet and throw together
our initial
>>>>ideas about a JSP/Struts based WDK.
>>>>
>>>>My sense is that our thinking compliments what you layed
out in your
>>>>Struts Demo.  Basically, we are buying into the ideas you
presented
>>>>about how the display can work.  We are also interested in
starting to
>>>>nail down the design of the underlying machinery (somewhat
along the
>>>>lines of what you outlined in your conclusions section). 
Much of our
>>>>thinking is informed by the current WDK design.
>>>>
>>>>We drew up a quick list of big-ticket requirements items,
some addressed
>>>>by your proposal and some not:
>>>>  - declarative specification of content, queries, dialogs.
>>>>
>>>>
>>>
>>>I follow the middle one. I'm not sure what you mean by
dialog and
>>> especially
>>>content through the email. Could you give a rough outline
of the Content
>>> bean?
>>>
>>>
>> By "content" we mean all kinds of verbiage on the site. 
The canonical
>> example is the tutorials available on the EpconDB site
>> (http://www.cbil.upenn.edu/EPConDB/).  The content is
considered "model"
>> not view.   The current implementation is Jonathan Schug's Page
>> Generator, which is written in perl.  The model is stored
in perl data
>> structures, independently from any formatting information,
and is
>> formated by the PageGenerator.  Its not always obvious
where to draw the
>> line between model and view.  Another example would be that
a home page
>> might have Introduction, News, Funding, etc. that we would
like to be in
>> the model.  Obviously, in the new WDK, model is stored in
Beans, and
>> view is stored mostly in JSP.
>>
>> By "dialog" we mean a form.  In the current WDK, the
dialogues are
>> specified declaratively in the servlet-config file.  They
are often
>> complex, with queries underlying pulldown lists, etc.  In
the new WDK we
>> were thinking we would have Dialog beans, or similar, to
manage these in
>> the model.
>>
>>>
>>>
>>>>  - configurable styles
>>>>
>>>>
>>>
>>>ie given an query syntax tree the way this is displayed to
the user
>>> should be
>>>easily modifiable, or something else?
>>>
>> Bear with me here.  I still haven't read the JSP book yet.
 But, the idea
>> is for the JSPs to refer to a stylesheet or similar, so
that we could
>> potentially reuse JSPs across projects.   An example would
be a JSP that
>> formats a query dialog.  The JSP is the same between, say,
allgenes and
>> plasmodb, but the look is different because of the style
configuration.  i
>> am not clear on how this relates to the tiles.
>>
>>>
>>>
>>>>  - site's standard s surrounding page specific stuff (ie,
your tiles
>>>>solution)
>>>>  - JavaScript functionality
>>>>
>>>>
>>>
>>>Server-side scripting or client side?
>>>
>>>
>> client side.  we use this for example to provide mouse-over
behaviour in
>> some of our graphics.
>>
>>>
>>>
>>>>  - calls to external resources (eg, processes) to provide
stuff like
>>>>graphics
>>>>  - boolean queries
>>>>  - history
>>>>  - report maker
>>>>
>>>>
>>>
>>>Is there a current implementation in one of the current GUS
sites or a
>>> spec
>>>somewhere? It's been mentioned at this end but I don't
think we ever went
>>> into
>>>it in much detail.
>>>
>> I guess you are refering to the ReportMaker.  It is alive
on the
>> Allgenes site.  Do a query, and then press Download from
the query
>> history.  The code is in two places.  The backend is in cvs
>> GUS/ReportMaker.  The frontend is still in our legacy CVS.
>>
>>>
>>>
>>>
>>>>  - batch submission
>>>>  - connection pooling
>>>>  - process pooling?
>>>>  - result caching
>>>>  - result paging
>>>>  - error handling
>>>>  - dialog validation
>>>>  - logging
>>>>
>>>>We sketched the following top level Beans, which we see
being configured
>>>>in config files (XML is fine... not sure yet about Digester)
>>>>
>>>>
>>>
>>>I only suggested that because that's what's used by Struts.
Played with
>>> it a
>>> bit more now and it seems simple to use for what we'd
want. But yes,
>>> there's
>>>any number of mature, open-source XML/Beans alternatives we
could go for
>>> instead.
>>>
>>>
>> Angel has looked at Digester and got the sense that it was
overkill.  i
>> haven't looked at it yet.  we remain open-minded.
>>
>>>>, and which
>>>>do not specify any formatting information:
>>>>  - Dialog  (eg, a form)
>>>>  - QueryDialog (a subclass of Dialog)
>>>>  - other subclasses of Dialog?
>>>>  - Record (eg, an RNA page and/or detailed page)
>>>>  - ResultSet (or is this just a record?)
>>>>
>>>>These guys have properties, which, are also beans, of types:
>>>>  - Content
>>>>  - SqlQuery
>>>>  - Process
>>>>
>>>>And, SqlQuery and Process have as properties subclasses of
Param, which
>>>>is also a bean.
>>>>
>>>>The main difference between the beans we see for the new
WDK and those
>>>>in the old WDK is that the new ones don't include any
formatting
>>>>information.  I think that means that we can have
siginificantly fewer
>>>>classes, because the classes don't have to differentiate
based on
>>>>formatting implementations.
>>>>
>>>>Based on our still rudimentary understanding of JSP, we
imagine these
>>>>kind of pages and fragments, which are somehow
parameterized by the
>>>> beans:
>>>>   - Dialog
>>>>   - QueryDialog
>>>>   - ResultSet
>>>>   - Record
>>>>   - Record Details
>>>>   - Content
>>>>
>>>>
>>>
>>>I suspect we may be thinking of two different things but
not sure. What
>>> kind of
>>>thing would content be as a page or page fragment wrt a
Content bean?
>>>
>>>
>>>
>> A Content fragment would be a JSP fragment that could show
news items.
>>
>>>
>>>
>>>>Things we are assuming JSP can do (haven't read the book
yet), and want
>>>>to understand more about:
>>>>  - bind beans to a JSP page
>>>>
>>>>
>>>
>>>Yep. jsp:useBean to tie a JavaBean to a page local
variable. We have to
>>> decide
>>>on a schedule and how cutting-edge we want to be. The
syntax becomes even
>>>clearer with JSP2.0 (eg Tomcat 5) but support for that is
still at
>>> alpha/beta
>>>for many containers. (There *should* be a stable
implementation in
>>> ~December for
>>>the official release of J2EE 1.4 so personally I don't
think it's
>>> unreasonable
>>>choice)
>>>
>>>
>> ok, lets keep that in mind.
>>
>>>
>>>
>>>>  - simple control features like iterate across a list of
results to
>>>> display
>>>>
>>>>
>>>
>>>Not part of JSP per se but there is a standard template
library that
>>> includes
>>>simple iterators, control flow etc. See
geneResults-body.jspf for an
>>> example
>>>
>>>
>>>
>>>>  - fetch JSP fragments to insert (eg, one per row of a
result)
>>>>
>>>>
>>>
>>>? Not sure I understand. There are two built-in include
mechanisms but
>>> for a
>>>table of results you'd generally write the formatting code
eg table tags
>>> as a
>>>template and insert the data into that. For the specific
case of the
>>>CellFormatter there is a working tag library equivalent in
the demo.
>>>
>>>
>>>
>>>>As far as the config files are concerned, we agree that
huge config
>>>>files are not optimal.  We don't yet see how best to
organize them,
>>>>though we want to be able to re-use some of them across
projects.  So, i
>>>>think they will need to find there way into a directory
structure of
>>>>some kind.
>>>>
>>>>Steveo
>>>>
>>>>
>>>
>>>Adrian
>>>
>>>
>>
>>
>>
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>-- 
>Sucheta Tripathy
>Virginia Bioinformatics Institute
>1880 pratt drive,Bldg XV
>Virginia tech.
>Blacksburg
>Virginia
>VA 24061
>phone-(540)231-8138
>
>
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Re: [Gusdev-gusdev] Struts documentation - supporting evidence

[<su...@vb...>]

Hi,
I am new to the GUS developer's forum, so I am not aware if the question
has already been addressed.

I was wondering in the table DoTS::NAFeatureImp (standard table), what are
the use of the int(1...), float(1..) and string attributes.

Is there a place where the meaning of the attributes has been documented?


Sucheta

> Adrian, see below.
>
> steve
>
> Adrian Roy Tivey wrote:
>
>>Hello,
>>
>>Thanks for your comments. Just a shortish email to expand on a couple of
>>points and request clarification on a couple of others (including
>> comments on
>>the first three points but that's just the order they happened to come
>> up!)
>>
>>
>>
>>>Adrian-
>>>
>>>Angel and I have had a chance to meet and throw together our initial
>>>ideas about a JSP/Struts based WDK.
>>>
>>>My sense is that our thinking compliments what you layed out in your
>>>Struts Demo.  Basically, we are buying into the ideas you presented
>>>about how the display can work.  We are also interested in starting to
>>>nail down the design of the underlying machinery (somewhat along the
>>>lines of what you outlined in your conclusions section).  Much of our
>>>thinking is informed by the current WDK design.
>>>
>>>We drew up a quick list of big-ticket requirements items, some addressed
>>>by your proposal and some not:
>>>  - declarative specification of content, queries, dialogs.
>>>
>>>
>>
>>I follow the middle one. I'm not sure what you mean by dialog and
>> especially
>>content through the email. Could you give a rough outline of the Content
>> bean?
>>
>>
> By "content" we mean all kinds of verbiage on the site.  The canonical
> example is the tutorials available on the EpconDB site
> (http://www.cbil.upenn.edu/EPConDB/).  The content is considered "model"
> not view.   The current implementation is Jonathan Schug's Page
> Generator, which is written in perl.  The model is stored in perl data
> structures, independently from any formatting information, and is
> formated by the PageGenerator.  Its not always obvious where to draw the
> line between model and view.  Another example would be that a home page
> might have Introduction, News, Funding, etc. that we would like to be in
> the model.  Obviously, in the new WDK, model is stored in Beans, and
> view is stored mostly in JSP.
>
> By "dialog" we mean a form.  In the current WDK, the dialogues are
> specified declaratively in the servlet-config file.  They are often
> complex, with queries underlying pulldown lists, etc.  In the new WDK we
> were thinking we would have Dialog beans, or similar, to manage these in
> the model.
>
>>
>>
>>>  - configurable styles
>>>
>>>
>>
>>ie given an query syntax tree the way this is displayed to the user
>> should be
>>easily modifiable, or something else?
>>
> Bear with me here.  I still haven't read the JSP book yet.  But, the idea
> is for the JSPs to refer to a stylesheet or similar, so that we could
> potentially reuse JSPs across projects.   An example would be a JSP that
> formats a query dialog.  The JSP is the same between, say, allgenes and
> plasmodb, but the look is different because of the style configuration.  i
> am not clear on how this relates to the tiles.
>
>>
>>
>>>  - site's standard s surrounding page specific stuff (ie, your tiles
>>>solution)
>>>  - JavaScript functionality
>>>
>>>
>>
>>Server-side scripting or client side?
>>
>>
> client side.  we use this for example to provide mouse-over behaviour in
> some of our graphics.
>
>>
>>
>>>  - calls to external resources (eg, processes) to provide stuff like
>>>graphics
>>>  - boolean queries
>>>  - history
>>>  - report maker
>>>
>>>
>>
>>Is there a current implementation in one of the current GUS sites or a
>> spec
>>somewhere? It's been mentioned at this end but I don't think we ever went
>> into
>>it in much detail.
>>
> I guess you are refering to the ReportMaker.  It is alive on the
> Allgenes site.  Do a query, and then press Download from the query
> history.  The code is in two places.  The backend is in cvs
> GUS/ReportMaker.  The frontend is still in our legacy CVS.
>
>>
>>
>>
>>>  - batch submission
>>>  - connection pooling
>>>  - process pooling?
>>>  - result caching
>>>  - result paging
>>>  - error handling
>>>  - dialog validation
>>>  - logging
>>>
>>>We sketched the following top level Beans, which we see being configured
>>>in config files (XML is fine... not sure yet about Digester)
>>>
>>>
>>
>>I only suggested that because that's what's used by Struts. Played with
>> it a
>> bit more now and it seems simple to use for what we'd want. But yes,
>> there's
>>any number of mature, open-source XML/Beans alternatives we could go for
>> instead.
>>
>>
> Angel has looked at Digester and got the sense that it was overkill.  i
> haven't looked at it yet.  we remain open-minded.
>
>>>, and which
>>>do not specify any formatting information:
>>>  - Dialog  (eg, a form)
>>>  - QueryDialog (a subclass of Dialog)
>>>  - other subclasses of Dialog?
>>>  - Record (eg, an RNA page and/or detailed page)
>>>  - ResultSet (or is this just a record?)
>>>
>>>These guys have properties, which, are also beans, of types:
>>>  - Content
>>>  - SqlQuery
>>>  - Process
>>>
>>>And, SqlQuery and Process have as properties subclasses of Param, which
>>>is also a bean.
>>>
>>>The main difference between the beans we see for the new WDK and those
>>>in the old WDK is that the new ones don't include any formatting
>>>information.  I think that means that we can have siginificantly fewer
>>>classes, because the classes don't have to differentiate based on
>>>formatting implementations.
>>>
>>>Based on our still rudimentary understanding of JSP, we imagine these
>>>kind of pages and fragments, which are somehow parameterized by the
>>> beans:
>>>   - Dialog
>>>   - QueryDialog
>>>   - ResultSet
>>>   - Record
>>>   - Record Details
>>>   - Content
>>>
>>>
>>
>>I suspect we may be thinking of two different things but not sure. What
>> kind of
>>thing would content be as a page or page fragment wrt a Content bean?
>>
>>
>>
> A Content fragment would be a JSP fragment that could show news items.
>
>>
>>
>>>Things we are assuming JSP can do (haven't read the book yet), and want
>>>to understand more about:
>>>  - bind beans to a JSP page
>>>
>>>
>>
>>Yep. jsp:useBean to tie a JavaBean to a page local variable. We have to
>> decide
>>on a schedule and how cutting-edge we want to be. The syntax becomes even
>>clearer with JSP2.0 (eg Tomcat 5) but support for that is still at
>> alpha/beta
>>for many containers. (There *should* be a stable implementation in
>> ~December for
>>the official release of J2EE 1.4 so personally I don't think it's
>> unreasonable
>>choice)
>>
>>
> ok, lets keep that in mind.
>
>>
>>
>>>  - simple control features like iterate across a list of results to
>>> display
>>>
>>>
>>
>>Not part of JSP per se but there is a standard template library that
>> includes
>>simple iterators, control flow etc. See geneResults-body.jspf for an
>> example
>>
>>
>>
>>>  - fetch JSP fragments to insert (eg, one per row of a result)
>>>
>>>
>>
>>? Not sure I understand. There are two built-in include mechanisms but
>> for a
>>table of results you'd generally write the formatting code eg table tags
>> as a
>>template and insert the data into that. For the specific case of the
>>CellFormatter there is a working tag library equivalent in the demo.
>>
>>
>>
>>>As far as the config files are concerned, we agree that huge config
>>>files are not optimal.  We don't yet see how best to organize them,
>>>though we want to be able to re-use some of them across projects.  So, i
>>>think they will need to find there way into a directory structure of
>>>some kind.
>>>
>>>Steveo
>>>
>>>
>>
>>Adrian
>>
>>
>
>
>
> -------------------------------------------------------
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> With VMware you can run multiple operating systems on a single machine.
> WITHOUT REBOOTING! Mix Linux / Windows / Novell virtual machines
> at the same time. Free trial click
> here:http://www.vmware.com/wl/offer/358/0
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-- 
Sucheta Tripathy
Virginia Bioinformatics Institute
1880 pratt drive,Bldg XV
Virginia tech.
Blacksburg
Virginia
VA 24061
phone-(540)231-8138