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Re: [Gusdev-gusdev] GUS 3.0 schema changes
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From: Angel P. <an...@sn...> - 2003-01-21 14:17:42
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The XML parsing is currently handled by the GUSRow module (formerly RelationalRow). As such, there are a few constraints on the creation of GUS XML objects, in addition to using the fully qualified object names. 1) It relies on newlines to get valid input. YOU MUST put object declaration on a separate line that attribute declarations. For instance the following do not work: <GUS::Model::RAD::Array><name> PancChip </name> </GUS::Model::RAD::Array> <GUS::Model::RAD::Array> <name> PancChip </name> <version> 1.2</version> </GUS::Model::RAD::Array> 2) To force a submit while parsing a GUS XML doc, enter the characters "//" on a separate line. I am not sure this is valid XML, but I suspect it is due to backwards compatability issues with SGML. I am working in my spare time (of which there is not much) to switch to an actual XML parser, rather than use of regular expressions (as is now the case). At the same time, I will swith the XML syntax to match a more database centric scheme, by using the tag attributes as the table columns, instead of subelements: <Object att1 = 'val1' att2 = 'val2' ... <Child Object .../> </Object> But this is not anywhere near finished (in fact just started) so for now we must live with the constaints as they stand. Angel On Mon, 20 Jan 2003, mazz wrote: > Dear Chris and Arnaud, > > It seems that it has changed. I think that perhaps Steve can clarify this. I > tested this bit of XML with the UpdateGusFromXML plugin, and although I can not > commit it to GUS30 now it recognized this tag designation for the table > (<GUS::Model::DoTS::GeneSynonym>).This plugin (UpdateGusFromXML) was recently > re-converted for GUS30. > > Arnaud, this is something I can completely clarify with you later. I still want > to go through and detemine what controlled vocabulary tables need to be populated > and create XML files for them (even if slight changes need to be made to the XML > later). > > Joan > > Chris Stoeckert wrote: > > > Joan, > > Right, the Perl packages used by the plugin indicate the directory tree > > that they are stored in but I thought the actual objects that the XML is > > used to populate directly reflect the database structure (not the > > directory structure) as they are generated from the tables. Has this > > changed? > > Chris > > > > On Mon, 20 Jan 2003, mazz wrote: > > > > > Chris, > > > > > > This is the designation for the table Object. > > > > > > package GUS::Model::DoTS::Gene; > > > > > > I thought this is what is needed for the table tag. > > > > > > Joan > > > > > > This is what it is for a RAD table > > > > > > package GUS::Model::RAD3::ElementAnnotation; > > > > > > > > > > > > > > > > > > Chris Stoeckert wrote: > > > > > > > Dear Joan and Arnaud, > > > > The CVS structure should not come into the XML used by the plug-in. It > > > > is my understanding that only the actual schema of the structure: > > > > Database.Namespace.Table.Attribute should be used. > > > > > > > > Chris > > > > > > > > On Monday, January 20, 2003, at 10:23 AM, mazz wrote: > > > > > > > > > Dear Arnaud, > > > > > > > > > > Model is a directory of Steve's new CVS structure under which the DoTS > > > > > table Objects (eg > > > > > > > > > > Gene) are found. > > > > > I do not know why Steve named the directory Model. > > > > > > > > > > Joan > > > > > > > > > > Arnaud Kerhornou wrote: > > > > > > > > > >> Hi Joan > > > > >> > > > > >> Thanks. Just a quick question, what is Model for ? > > > > >> > > > > >> <GUS::Model::DoTS::Gene> > > > > >> > > > > >> Arnaud > > > > >> > > > > >> mazz wrote: > > > > >> > > > > >>> Hi Arnaud, > > > > >>> > > > > >>> > > > > >>> Below is a sample of the XML for a table (e.g. Gene) the plugin > > > > >>> will > > > > >>> use. > > > > >>> The controlled vocabulary table DoTS::EffectorActionType also needs > > > > >>> to > > > > >>> be populated. > > > > >>> > > > > >>> I will try to go though and make a list of the new controlled > > > > >>> vocabulary > > > > >>> tables. > > > > >>> Tables such as geneCategory & rnaCategory are tables I created for my > > > > >>> planned future annotation tasks. > > > > >>> > > > > >>> > > > > >>> Joan > > > > >>> > > > > >>> <GUS::Model::DoTS::Gene> > > > > >>> <gene_id>10288603</gene_id> > > > > >>> <name>test</name> > > > > >>> <review_status_id>1</review_status_id> > > > > >>> <description>gene desc test</description> > > > > >>> <reviewer_summary>test</reviewer_summary> > > > > >>> </GUS::Model::DoTS::Gene> > > > > >>> > > > > >>> Arnaud Kerhornou wrote: > > > > >>> > > > > >>> Arnaud Kerhornou wrote: > > > > >>> > > > > >>> > > > > >>> > > > > >>>> Hi Joan > > > > >>>> > > > > >>>> I'll get the new controlled vocabularies ready for population. If > > > > >>>> you're planning to use the UpdateFromXML.pm plugin for populating > > > > >>>> GUS > > > > >>>> I should have examples. > > > > >>>> > > > > >>>> Regarding ComplexType it should be covered by GO component. > > > > >>>> Regarding InteractionType, we need to find a controlled vocabulary > > > > >>>> which I'm not aware of yet ! > > > > >>>> > > > > >>>> cheers > > > > >>>> Arnaud > > > > >>>> > > > > >>>> mazz wrote: > > > > >>>> > > > > >>>> > > > > >>>> > > > > >>>>> Hi Jonathan, > > > > >>>>> > > > > >>>>> Perhaps we can ask Matt to revisit his documentation plugin. There > > > > >>>>> are probably > > > > >>>>> additional changes he will have to make for its use with GUS30 now. > > > > >>>>> Also, I can send Arnaud an example of the XML for a table. We can > > > > >>>>> use the XML to > > > > >>>>> populate the rows of the controlled vocabulary tables (ids, terms > > > > >>>>> (names) and > > > > >>>>> definitions (descriptions). > > > > >>>>> > > > > >>>>> > > > > >>>>> Joan > > > > >>>>> > > > > >>>>> Jonathan Crabtree wrote: > > > > >>>>> > > > > >>>>> > > > > >>>>> > > > > >>>>> > > > > >>>>>> Hi Joan- > > > > >>>>>> > > > > >>>>>> Arnaud did supply us with documentation (attached) for the new > > > > >>>>>> Phenotype tables, > > > > >>>>>> but I just haven't loaded it into the database yet (I've also been > > > > >>>>>> quite busy :)) > > > > >>>>>> I started working on updating the documentation a couple of days > > > > >>>>>> ago, but in the > > > > >>>>>> process discovered that there are some invalid rows in > > > > >>>>>> core.DatabaseDocumentation > > > > >>>>>> that should be corrected first. A query shows that there are 73 > > > > >>>>>> rows in this > > > > >>>>>> table that reference nonexistent columns in GUS 3.0. For the most > > > > >>>>>> part I think > > > > >>>>>> that these are relatively minor problems stemming from the fact > > > > >>>>>> that the schema > > > > >>>>>> has been updated more recently than the documentation. However, > > > > >>>>>> there are also > > > > >>>>>> a few rows that suggest we need to improve the plugin and/or > > > > >>>>>> procedure used to > > > > >>>>>> populate this table. For example, the following rows have spaces > > > > >>>>>> in the column > > > > >>>>>> name (attribute_name), probably because the input files were > > > > >>>>>> invalid and the plugin > > > > >>>>>> has no restrictions on the format of the attribute_name: > > > > >>>>>> > > > > >>>>>> DATABASE_DOCUMENTATION_ID > > > > >>>>>> ------------------------- > > > > >>>>>> ATTRIBUTE_NAME > > > > >>>>>> ------------------------------------------------------------------ > > > > >>>>>> -------------- > > > > >>>>>> 1419 > > > > >>>>>> bio_material_id fk to LabelledExtract view of BioMaterial > > > > >>>>>> > > > > >>>>>> 1103 > > > > >>>>>> bio_source_characteristic_id primary key > > > > >>>>>> > > > > >>>>>> 1120 > > > > >>>>>> treatment_id fk to Treatment > > > > >>>>>> > > > > >>>>>> DATABASE_DOCUMENTATION_ID > > > > >>>>>> ------------------------- > > > > >>>>>> ATTRIBUTE_NAME > > > > >>>>>> ------------------------------------------------------------------ > > > > >>>>>> -------------- > > > > >>>>>> 1374 > > > > >>>>>> review_status_id The identifer of the review status > > > > >>>>>> > > > > >>>>>> 1418 > > > > >>>>>> assay_id fk to Assay > > > > >>>>>> > > > > >>>>>> 1373 > > > > >>>>>> synonym_name The gene symbol > > > > >>>>>> > > > > >>>>>> 6 rows selected. > > > > >>>>>> > > > > >>>>>> Also, as an aside (and not a comment to you in particular), it > > > > >>>>>> strikes me that > > > > >>>>>> column "documentation" of the form "fk to Table X" and "Primary > > > > >>>>>> key" could be > > > > >>>>>> generated automatically from the schema. However, comments on > > > > >>>>>> foreign keys > > > > >>>>>> are useful if they identify the specific subclass (i.e. view) to > > > > >>>>>> which the > > > > >>>>>> reference is expected to link, or if they explain what the > > > > >>>>>> referenced value is > > > > >>>>>> used for (if not obvious). Anyway, since there are still some > > > > >>>>>> minor schema > > > > >>>>>> changes taking place, I think that next week might be a good time > > > > >>>>>> to worry > > > > >>>>>> about updating all the documentation, since the database will be > > > > >>>>>> locked down > > > > >>>>>> for the migration at that point anyway. As for the controlled > > > > >>>>>> vocabularies, > > > > >>>>>> I think you're right, and we should try to populate these as soon > > > > >>>>>> as we can, > > > > >>>>>> even if it will be an iterative process in some cases. > > > > >>>>>> > > > > >>>>>> Jonathan > > > > >>>>>> > > > > >>>>>> > > > > >>>>>> > > > > >> > > > > >> ------------------------------------------------------- > > > > >> This SF.NET email is sponsored by: FREE SSL Guide from Thawte > > > > >> are you planning your Web Server Security? Click here to get a FREE > > > > >> Thawte SSL guide and find the answers to all your SSL security > > > > >> issues. > > > > >> http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > > > > >> _______________________________________________ > > > > >> Gusdev-gusdev mailing list > > > > >> Gus...@li... > > > > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > > This SF.NET email is sponsored by: FREE SSL Guide from Thawte > > > > > are you planning your Web Server Security? Click here to get a FREE > > > > > Thawte SSL guide and find the answers to all your SSL security issues. > > > > > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > > > > > _______________________________________________ > > > > > Gusdev-gusdev mailing list > > > > > Gus...@li... > > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > > ------------------------------------------------------- > > > > This SF.NET email is sponsored by: FREE SSL Guide from Thawte > > > > are you planning your Web Server Security? Click here to get a FREE > > > > Thawte SSL guide and find the answers to all your SSL security issues. > > > > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > > > > _______________________________________________ > > > > Gusdev-gusdev mailing list > > > > Gus...@li... > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > ------------------------------------------------------- > > > This SF.NET email is sponsored by: FREE SSL Guide from Thawte > > > are you planning your Web Server Security? Click here to get a FREE > > > Thawte SSL guide and find the answers to all your SSL security issues. > > > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > > > _______________________________________________ > > > Gusdev-gusdev mailing list > > > Gus...@li... > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > -- > > Chris Stoeckert, Ph.D. > > Research Associate Professor, Dept. of Genetics > > Center for Bioinformatics, University of Pennsylvania > > 423 Guardian Dr., Philadelphia, PA 19104 > > Ph: 215-573-4409 FAX:215-573-3111 > > > > ------------------------------------------------------- > > This SF.NET email is sponsored by: FREE SSL Guide from Thawte > > are you planning your Web Server Security? Click here to get a FREE > > Thawte SSL guide and find the answers to all your SSL security issues. > > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > ------------------------------------------------------- > This SF.NET email is sponsored by: FREE SSL Guide from Thawte > are you planning your Web Server Security? Click here to get a FREE > Thawte SSL guide and find the answers to all your SSL security issues. > http://ads.sourceforge.net/cgi-bin/redirect.pl?thaw0026en > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Angel Pizarro Programmer Analyst Center for Bioinformatics an...@pc... |
