Include filenames in loc file DEBUG lines

[peterjc]

This will help debugging where multiple (possibly conflicting) *.loc files come from, e.g.

$ grep blastdb paster.log
...
galaxy.tools.data DEBUG 2016-10-25 18:34:50,841 Loaded tool data table 'blastdb_p'
galaxy.tools.data DEBUG 2016-10-25 18:34:51,356 Loaded tool data table 'blastdb'
galaxy.tools.data DEBUG 2016-10-25 18:34:51,359 Loading another instance of data table 'blastdb_p', attempting to merge content.
galaxy.tools.data DEBUG 2016-10-25 18:34:51,375 Loaded tool data table 'blastdb_d'
...

Evidently I may have at least two copies of blastdb_p.loc, but where are they?

With the patch:

$ grep blastdb paster.log
...
galaxy.tools.data DEBUG 2016-10-25 18:43:48,947 Loaded tool data table 'blastdb_p' from file './config/tool_data_table_conf.xml.sample'
galaxy.tools.data DEBUG 2016-10-25 18:43:49,729 Loaded tool data table 'blastdb' from file './config/shed_tool_data_table_conf.xml'
galaxy.tools.data DEBUG 2016-10-25 18:43:49,733 Loading another instance of data table 'blastdb_p' from file './config/shed_tool_data_table_conf.xml', attempting to merge content.
galaxy.tools.data DEBUG 2016-10-25 18:43:49,736 Loaded tool data table 'blastdb_d' from file './config/shed_tool_data_table_conf.xml'
...

I am now puzzled about why blastdb_p gets loaded twice from the XML:

$ grep blastdb config/shed_tool_data_table_conf.xml
<table comment_char="#" name="blastdb">
        <file path="/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb.loc" />
<table comment_char="#" name="blastdb_p">
        <file path="/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_p.loc" />
<table comment_char="#" name="blastdb_d">
        <file path="/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_d.loc" />

[nsoranzo]

I am now puzzled about why blastdb_p gets loaded twice from the XML:

@peterjc It's loaded from 2 different files:
./config/tool_data_table_conf.xml.sample
./config/shed_tool_data_table_conf.xml

Or am I misreading your comment?

[peterjc]

I understand it now - tool_data_table_conf.xml.sample ships with Galaxy and currently includes the (nucleotide) blastdb.loc file, while all three database *.loc table definitions ship with the BLAST datatypes from the Tool Shed (pending peterjc/galaxy_blast#75 moving them back into the Galaxy core).

[peterjc]

To expand on my last comment, I now fully understand the inconsistency between the difference blastdb*.loc files, and #3098 should fix it.

[chambm]

I was just going to suggest this feature; instead I need to wait for Galaxy Jetstream to be updated, or figure out how to do it myself. 👍