GitLab

We didn't declare that this essential script would be removed in release
65, so we're keeping it around until after the release. The new script,
schema_patcher.pl, will live alongside it.

toplevel location code can now deal with excessively large regions and shrinks them down to size if possible or rejects them.

Updated the metazoan set of species, adding tribolium_castaneum strongylocentrotus_purpuratus nematostella_vectensis bombyx_mori amphimedon_queenslandica atta_cephalotes

user didn't specify a species name on the command line.

With --fix:
        If the databse has no patch identifiers recorded, start fix at
        schema_version.

        Do apply the 'a' patches, but warn the user that these may reset
        the schema_version.

Correct two faulty regexes.

find a patch the default.

schema_version.

+    When the --fix command line switch is used, the script will also
+    make it possible to apply older patches that might have been
+    skipped.  For example: A database at schema version 65, with patches
+    since release 40, will not only be patched to the appropriate
+    release (specified with --release=NN), but all patches since release
+    40 (inclusively) will be tested.  If the patch identifier for an old
+    patch is missing from the meta table of the database, that patch
+    will be applied.

incremental patches from arbitrary old release.  Support for core,
variation and funcgen schemas is implemented.

Run without arguments to get usage info, and with --about for further
info.

useful script to get the external databases references for a gene or transcript using either the stable_id or the gene name

/software/perl-5.8.8/bin is picked up automatically.
This doesn't work if people change the #! lines in
the top of the scripts (so don't do that).

- you can use the @colour tag in the @header block
- you can use a @legend tag to fill automatically the Colour legend table

load_XXXX() methods now return the number of adaptors which have appeared in the registry due to that method's invocation. This can be used to report success or failure to load databases.

Improving the error handling of the DBI connection in load_registry_from_db(). We now report an error if it cannot connect to the MySQL DB and if it was not pingable. Hopefully this catches both erronious scenarios.