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Re: [Gusdev-gusdev] class notdefyet??
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From: Michael L. <lu...@ug...> - 2004-06-17 14:19:35
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Here you go:
We wanted to enter new data into GUS. Mass Spec data. This required
the use of a plug-in that was provided by Martin Fraunholz. The plugin
needed two perl modules that we did not have. DoTS::MassSpecSummary and
DoTS::MassSpecFeature. These are plug-ins of the type that are
automatically generated by a gus install with regards to the tables that
are in the GUS schema
We did not have these modules in our $GUS_HOME/lib/perl/GUS/Model/DoTS/
directory, because we did not have these tables in our schema.
Obviously
this required us to update our gus installation.
So this is what we did:
1. Create the tables
* Very important to add the primary key constraints
2. Add the tables description to Core.TableInfo
* Very important to describe correctly the table for perl objects
automatic generation
3. Download GUS from CVS
4. Build
* If the build resets all sequences to 1, we have a clue on how to
fix them.
Describing the steps in detail:
1. Create the tables:
If the table that you want to create has been incorporated into later
versions of GUS, then chances are you can find the sql to create the
table somewhere in the latest version of GUS from CVS.
Look in
$PROJECT_HOME/GUS/Model/schema/oracle/
There are 6 types of files containing the sql commands for each schema.
For example, for DoTS schema:
dots-constraints.sql
dots-indexes.sql
dots-pkey-constraints.sql
dots-sequences.sql
dots-tables.sql
dots-views.sql
- Create table commands
create table dots.massspecsummary(
mass_spec_summary_id number(12) not null,
aa_sequence_id number(12) not null,
prediction_algorithm_id number(12) not null,
external_database_release_id number(12) null,
developmental_stage varchar2(20) not null,
is_expressed number(1) not null,
number_of_spans number(12) not null,
sequence_count number(12) not null,
spectrum_count number(12) not null,
aa_seq_percent_covered float(22) not null,
aa_seq_length number(12) not null,
aa_seq_molecular_weight number(12) not null,
aa_seq_pi float(22) not null,
modification_date date not null,
user_read number(1) not null,
user_write number(1) not null,
group_read number(1) not null,
group_write number(1) not null,
other_read number(1) not null,
other_write number(1) not null,
row_user_id number(12) not null,
row_group_id number(3) not null,
row_project_id number(4) not null,
row_alg_invocation_id number(12) not null)
storage( maxextents unlimited );
- Add the primary key constraints.
If the table has a primary key, you must make sure to enter the
constraint.
alter table dots.massspecsummary add constraint
PK_MASSSPECSUMARY
primary key (MASS_SPEC_SUMMARY_ID);
- Add the foreign key constraints, create the views, indexes, and
sequences. Again the sql for this can usually be found somewhere in
$PROJECT_HOME/GUS/Model/schema/oracle/
2. Add the tables description to Core.TableInfo
The description of the new tables then need to be entered into
Core.TableInfo, since this is the place that the GUS installation will
look for tables to automatically create modules for. It is imperative
that you set the attributes correctly, otherwise the build will not
work.
table_id -> Unique identifier to the tables (automatic generated by
SubmitRow plug-in).
name -> Name of the table without the schema prefix 'Schema::'. eg: for
DoTS::MassSpecSummary, the table name is MassSpecSummary.
table_type -> controlled vocabulary, many to many, standard, version,
view.
primary_key_column -> Which is the column from this new table you're
describing that identifies uniquely the data inside? (This column must
be set as primary key on the database schema)
database_id -> Here you supply information about the schemas Core, DoTS,
SRes, RAD3, TESS. You must provide the database_id for the correct entry
in the Core.DatabaseInfo table.
is_versioned -> If the table is to be in a Ver schema.
is_view -> This must be set to 1 if you're describing a view. Otherwise,
set it to 0.
view_on_table_id -> Insert the table_id of the table where your new view
gets its data, null otherwise.
superclass_table_id -> Insert the table_id of the table of which your
new table is a child, null if it is not a child table.
is_updatable -> this seems to always be set to 1.
Example:
ga GUS::Common::Plugin::SubmitRow
--tablename Core::TableInfo
--attrlist
"name,table_type,primary_key_column,database_id,is_versioned,is_view,is_updatable"
--valuelist
"MassSpecSummary^^^standard^^^mass_spec_summary_id^^^5^^^0^^^0^^^1"
3. Download GUS from CVS
Go ahead and get the latest version. You might want to make a
back up copy of what
you presently have.
4. Build
If you have customized some modules, you might want to make back-ups of
them in a temporary directory.
The last step is to rebuild the GUS installation by executing the
command:
build GUS install -append
Our first attempt to rebuild reset all our sequences to 1. We developed
a perl script to autofix all sequences based on the primary_keys current
value. But this is not supposed to happen with the latest version of
GUS from CVS.
If it happens, it is an easy fix. Just ask for the script...
On Wed, 2004-06-16 at 13:20, Sucheta Tripathy wrote:
> Hi Michael,
>
> I am sure I will find my answer if I browse through the source forge page,
> but just to get a qucik answer I am writing to you.In case you have some
> time please address this.
>
> I know you added some tables and re-generated the objects, I just wanted
> to make sure what is the sequence of events.
>
> I understand it to be
>
> 1. Change the table definition
> 2. Rebuild the schema by giving install -append option.
>
> In our case I have the old CVS, not updated. I am afraid if I will be
> stuck at the re building stage. And also what happens to the plugins that
> are modified by us locally.And also what happens to the data already
> present in the tables?
>
>
>
> Many thanks
>
> Sucheta
>
> > No worry about this.
> > The class was not defined because I had not done the following:
> > alter table dots.massspecsummary add constraint PK_MASSSPECSUMMARY
> > primary key\
> > (mass_spec_summary_id);
> >
> >
> > On Wed, 2004-06-16 at 11:01, Michael Luchtan wrote:
> >> Hello-
> >> Is this class some kind of standard notation for the gus development
> >> team? I would assume that it means that the class has not been defined
> >> yet. I get the following error message sometimes when trying to run
> >>
> >> build GUS install -append
> >>
> >> [javac] Compiling 1095 source files to
> >> /var/local/checkout/GUS/Model/classes
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : class notdefyet
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] notdefyet pk = get();
> >> [javac] ^
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : method get ()
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] notdefyet pk = get();
> >> [javac] ^
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:312:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : method get ()
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] notdefyet pk = get();
> >> [javac] ^
> >> [javac]
> >> /var/local/checkout/GUS/Model/src/java/org/gusdb/model/DoTS/MassSpecSummary_Row.java:320:
> >> \
> >> cannot resolve symbol
> >> [javac] symbol : class notdefyet
> >> [javac] location: class org.gusdb.model.DoTS.MassSpecSummary_Row
> >> [javac] set(new notdefyet(pk));
> >> [javac] ^
> >> [javac] 3 errors
> >>
> >> BUILD FAILED
> >> file:/var/local/checkout/install/build.xml:235: Compile failed; see the
> >> compiler error output for deta\
> >> ils.
> >>
> >> Am I doing something wrong that would cause this class to not be
> >> defined, or is this just part of the latest version from CVS?
> >
> >
> >
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