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OraCIF GENERATOR  is a set of programs that  generates other programs that are then used by other components of the OraCIF package. 

The  Generator takes the list of mmCIF categories present in the mapping metadatabase and for each category  creates two database  stored procedures for extracting data and presenting it as mmCIF and Xml respectively. These procedures are then used by other components of OraCIF although it is possible for users to access them directly should they wish.

INPUTS

The Generator   takes input information about the mmCIF dictionary, the macromolecular structural database(s) and the mapping between them.  This input information is supplied as database tables and the location of each these tables is specified in a parameter   table.   

The mmCIF dictionary and supplements. 

The Generator requires a database version  of the mmCIF dictionary. Currently all the mmCIF files exported are compliant with the PDB mmCIF Extension  Dictionary that was  developed for this purpose as part of TEMBLOR work package WP9.7. The extended ebi_style  DDL was used that includes basic information about the presentation of the mmCIF categories.  However, through this dictionary table (and the associated  mapping metadatabase) it is possible to configure OraCIF to export  mmCIF files compliant with other mmCIF dictionaries. 

The mapping metadatabase.   

The Generator also requires a mapping database  that contains the information on how  the organization of the source database(s) maps  onto the organization of the  mmCIF files as described by the mmCIF dictionary. The mapping metadatabase may contain many mappings, termed 'roles', that allow OraCIF to be configured to  export data  to different  mmCIF specifications. 

The Source Database(s). 

The Generator also requires access to the tables in the source database(s) from  which  data will eventually be extracted. This allows the Generator to check  that the tables and columns that will be accessed  by the generated procedures actually exist  and to ensure that the generated procedures will be valid. It is not necessary for the extracted data  to be held in a single database schema and indeed this is frequently not the case.   

Xml formatting details. 

If Xml output is required  then details of the structure of Xml should also be provided. 

PROCESS

The Generator runs through  a series of steps 

Validating  the mapping. 

The Generator first checks that the chosen mapping is consistent both with the mmCIF dictionary  and with the structure of the target database(s).          

Generation of Stored Procedures. 

The stored procedures themselves are then generated. It is possible to set the Generator to either   create a complete new set of stored procedures (one each for export mmCIF and XML for ach mmCIF category present in the mapping metadatabase) or else  specifically to regenerate a single stored procedure - useful when a only a single aspect of the mapping has been changed.   

Status tracking. 

OraCIF keeps track of the validation and generation procedures, catching any errors thrown by these processes. OraCIF also tracks whether the mappings or the structure of the target database(s) have been change since the last generation of the stored procedures which facilities synchronising  the stored procedures with the various inputs (source database structure, mmCIF dictionary, metadatabase).

OUTPUTS

The Generator produce a permanent set of database stored  procedures in Pl/Sql and Pl/SqlX and the list of problems if  any of them  is not generated.