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[Gusdev-gusdev] Understanding Imp tables
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From: Steve F. <sfi...@pc...> - 2003-09-04 18:13:00
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[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 > > |
