Title:  Loading of new FPC data from Cari
Author: Ken Y. Clark 
Date:   01-Oct-2002

1.  Cron job retrieves new FPC data into "/dir/for/original/fpc/data" 
    on chevre naming the file according to the date of fetching.

2.  Script parses data into format acceptable for import by cmap_admin.pl, 
    places output into "/dir/for/cmap/fpc/import," naming the file for
    the date of importing.

    Options:

    A)  Check that markers are only of four types:

        1)  Hybridization
        2)  New Marker from Gramene anlysis
        3)  Confirmed by our analysis
        4)  Existing but not on the same clone

    B) Uppercase all feature names

3.  Switch database connection string in "cmap.conf" on chevre to use
    alternate schema ("cmap" or "cmap1").

4.  Use cmap_admin.pl on chevre to:

    A)  Reload data into alternate schema, log activity (inserts, updates)
    B)  Reimport correspondence file
    C)  Rerun name-based correspondences
    D)  Regenerate matrix data

5.  Run script to compare numbers between two schemas.

    Options:
    
    A)  Only check numbers related to new FPC map set (not every map set)
    
    B)  Give the following statisitics:

        1)  Total number of maps (contigs)
        2)  Total number of features by feature type (e.g., markers, clones)
        3)  Number of features on each map by feature type
        4)  Total number of correspondences by type (e.g., insilico, name-based)
        5)  Number of correspondences by type from new set to every other set

6.  Curator verifies and corrects new data:

    A)  Use cmap_admin.pl log file and output of above script
    B)  Visualize each major linkage group for the major reference
        genetic maps with the new FPC map.
    C)  Edit questionable marker correspondences; send file of curated
        suggestions and supporting evidence to Cari
    D)  Check style consistency (map names, feature names, case
        sensitivity, duplicates of feature types on maps)
    E)  Check links for several of the new features added to the
        database (new features can be found by inspecting log of
        cmap_admin.pl).

7.  If data is correct:

    A)  Leave database switched to new data source.  
    B)  Ask DBA to copy new schema on chevre to raclette. If possible,
        copy only to "cmap" namespace on raclette; alternately copy to
        whatever namespace is convenient and switch "cmap.conf" on brie4
        to point to new schema name and restart Apache.

8.  If data is not correct:

    A)  Switch back to previous data source
    B)  Ask DBA to copy original schema over backup, correct the data,
        restart import process.