Re: [Gusdev-gusdev] class notdefyet??

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michael-

would you consider putting this on the gus wiki?

steve

Michael Luchtan wrote:

>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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>>>      
>>>
>
>
>
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