Log loading of resources from *.loc files #3099
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nsoranzo
reviewed
Oct 26, 2016
| @@ -465,6 +465,8 @@ def parse_file_fields( self, reader, errors=None, here="__HERE__" ): | |||
| if errors is not None: | |||
| errors.append( line_error ) | |||
| log.warning( line_error ) | |||
| if hasattr(reader, "name"): | |||
| log.info("Loaded %i lines from '%s' for '%s'", len(rval), reader.name, self.name) | |||
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log.debug seems indeed more appropriate.
|
As suggested and seconded by @nsoranzo, switched to logging this at debug level instead (branch updated with force push). |
Example output: ``` $ grep "lines from" paster.log galaxy.tools.data DEBUG 2016-10-26 10:24:22,742 Loaded 0 lines from 'tool-data/all_fasta.loc' for 'all_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,753 Loaded 0 lines from 'tool-data/bfast_indexes.loc' for 'bfast_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,848 Loaded 24 lines from 'tool-data/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:22,859 Loaded 0 lines from 'tool-data/maf_index.loc' for 'indexed_maf_files' galaxy.tools.data DEBUG 2016-10-26 10:24:22,865 Loaded 0 lines from 'tool-data/ngs_sim_fasta.loc' for 'ngs_sim_fasta' galaxy.tools.data DEBUG 2016-10-26 10:24:22,878 Loaded 0 lines from 'tool-data/perm_base_index.loc' for 'perm_base_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,890 Loaded 0 lines from 'tool-data/perm_color_index.loc' for 'perm_color_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,895 Loaded 0 lines from 'tool-data/picard_index.loc' for 'picard_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,899 Loaded 0 lines from 'tool-data/picard_index.loc' for 'srma_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,937 Loaded 0 lines from 'tool-data/mosaik_index.loc' for 'mosaik_indexes' galaxy.tools.data DEBUG 2016-10-26 10:24:22,943 Loaded 0 lines from 'tool-data/twobit.loc' for 'twobit' ... galaxy.tools.data DEBUG 2016-10-26 10:24:24,036 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb.loc' for 'blastdb' galaxy.tools.data DEBUG 2016-10-26 10:24:24,106 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_p.loc' for 'blastdb_p' galaxy.tools.data DEBUG 2016-10-26 10:24:24,112 Loaded 0 lines from '/mnt/shared/galaxy/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/7f3c448e119b/blastdb_d.loc' for 'blastdb_d' ```
|
Thank you @peterjc, this should indeed be helpful. |
|
Great - it already helped me resolve why some of my |
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Example output:
I'm happy to make this a DEBUG log entry, rather than info level as implemented.
The reason for logging this is to help Galaxy administrators struggling with
*.locfiles failing to take effect - in my casetool-data/blastdb_p.locis loading buttool-data/blastdb.locandtool-data/blastdb_d.locappear to be ignored, see also #3095 and #3098