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This page is pulled directly from the README.Apollo documentation in the Chado code repository and is converted to text and dynamically loaded in this page. The README was most recently changed on Thursday 21st of September 2006 01:26:42 PM

Reading and Writing to a Chado database with Apollo
    This needs to be better documented, but here is a start:

    In order to use Apollo read/write with chado, here are things that need
    to be done:

    Grant privileges to users to several tables (list here)
        In the absense of a complete list of tables, you can grant access to
        all tables using sqlt and the perl Template::Toolkit template,

            sqlt -f PostgreSQL -t TTSchema --template bin/privileges.tmpl modules/nofuncs.sql | psql

        You can edit the template to grant privileges to just specific users
        instead of PUBLIC, which of course would be a lot more secure.

    Insert several ad hoc cv terms found in
        This file contains sql commands to insert several controlled
        vocabulary terms that Apollo expects to be in the database. This
        file can be recreated with additional terms as needed by editing the
        file modules/sequence/apollo-bridge/ad_hoc_cv and running the perl
        script modules/sequence/apollo-bridge/ The
        resulting sql file can be inserted into the database with this

            $ psql $DBNAME < modules/sequence/apollo-bridge/cv_inserts.sql

    Insert a few misc items like those found in
        Essentially, Apollo and chado have to agree about what the names of
        the programs in the analysis table are, and there needs to be a few
        terms in the cv table.

        About naming analysis results: there are no restrictions on what you
        name them, however the GFF3 bulk loader will insert them typically
        one of two ways:

        1   If you specify the -a (--analysis) flag with an argument, the
            loader will look for an entry in the analysis table where
   is equal to the argument supplied with -a.

        2   If you don't give an argument with -a, the loader will look for
   that is equal to the GFF source and type
            concatentated with and underscore between them, ie
            'source_type', eg, 'Rice_cDNA_match'.

        The inserts into the db table are there so that dbxref entries in
        GFF files I typically process. They can be ignored unless you are
        loading GFF files with Dbxref entries.

        Then there is the uniquename_id_generator sequence, for which
        integers for building uniquenames are used. Then there are two
        interts in to cvtermprop for the suffix and prefix for uniquename
        generation. Generated uniquenames with be of the form:

            $prefix . (int from uniquename_id sequence) . $suffix

        For exmple, if you insert 'RICE' for the prefix and 'X' for the
        suffix, the resulting name of the first feature will be

    Add the functions and triggers to chado.
        Use the perl script:

            % /usr/local/bin/ create

        Note that this script can also be used to drop and add the triggers
        in case you want to do some bulk loading and want to disactivate the
        triggers for that.

    Modify the Apollo configuration file, chado-adapter.xml.
        is a section for connecteding directly to flybase chado in the
        apollo doc directory: doc/html/userguide.html but it is somewhat out
        of date. I need to work with Mark to update it (it will probably
        need me to write it and have Mark proof it).

    I understand that these directions are somewhat vague. Getting Apollo to
    work with chado requires a little hands on tinkering. If you find
    yourself having difficulties, please contact me.

    Scott Cain