Change TaxonomyProvider useCache to True in MMseqsUtils

[piehld]

Or add a reload() and testCache method to determine if should rebuild from scratch (in MMseqsUtils.py).

Currently, in etl.build_exdb_resources.UpdateTargetsCofactors, the taxonomy data is downloaded 6 times in a row (https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz):

... running   UpdateTargetsCofactors()
2023-09-19 08:57:32,208 - luigi-interface - INFO - [MainThread] - Starting workflow ProteinTargetSequenceExecutionWorkflow (full)
2023-09-19 08:57:33,444 - root - INFO - [MainThread] - Running cacheTaxonomy...
2023-09-19 08:57:35,886 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy primary fetch status (True) using 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
2023-09-19 08:58:16,205 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy lengths name 2528571 node 2528676 merge 73969
...
...
2023-09-19 09:59:32,570 - root - INFO - [MainThread] - Running searchDatabases...
2023-09-19 09:59:39,341 - __name__ - INFO - [MainThread] - convertalis status is True
2023-09-19 09:59:39,697 - __name__ - INFO - [MainThread] - Starting search result with (8531) records
2023-09-19 09:59:39,733 - __name__ - INFO - [MainThread] - Query match count 742
2023-09-19 09:59:39,733 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Query sequences with matches 'sabdab' (742) bitScore filter (False)
2023-09-19 09:59:40,046 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Completed searching sabdab targets (status True) (cutoff=0.95) at 2023 09 19 09:59:40 (7.4758 seconds)
2023-09-19 10:00:05,435 - __name__ - INFO - [MainThread] - convertalis status is True
2023-09-19 10:00:09,308 - __name__ - INFO - [MainThread] - useTaxonomy flag (True)
2023-09-19 10:00:13,438 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy primary fetch status (True) using 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
2023-09-19 10:00:36,127 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy lengths name 2528571 node 2528676 merge 73969
2023-09-19 10:00:36,127 - __name__ - INFO - [MainThread] - Starting search result with (89015) records
2023-09-19 10:00:37,255 - __name__ - INFO - [MainThread] - Query match count 2839
2023-09-19 10:00:37,259 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Query sequences with matches 'card' (2839) bitScore filter (False)
2023-09-19 10:00:42,039 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Completed searching card targets (status True) (cutoff=0.95) at 2023 09 19 10:00:42 (61.9924 seconds)
2023-09-19 10:01:24,274 - __name__ - INFO - [MainThread] - convertalis status is True
2023-09-19 10:01:28,952 - __name__ - INFO - [MainThread] - useTaxonomy flag (True)
2023-09-19 10:01:32,687 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy primary fetch status (True) using 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
2023-09-19 10:02:09,622 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy lengths name 2528571 node 2528676 merge 73969
2023-09-19 10:02:09,622 - __name__ - INFO - [MainThread] - Starting search result with (106156) records
2023-09-19 10:02:11,032 - __name__ - INFO - [MainThread] - Query match count 4180
2023-09-19 10:02:11,036 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Query sequences with matches 'drugbank' (4180) bitScore filter (False)
2023-09-19 10:02:16,465 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Completed searching drugbank targets (status True) (cutoff=0.95) at 2023 09 19 10:02:16 (94.4264 seconds)
2023-09-19 10:03:54,283 - __name__ - INFO - [MainThread] - convertalis status is True
2023-09-19 10:04:02,151 - __name__ - INFO - [MainThread] - useTaxonomy flag (True)
2023-09-19 10:04:05,087 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy primary fetch status (True) using 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
2023-09-19 10:04:45,656 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy lengths name 2528571 node 2528676 merge 73969
2023-09-19 10:04:45,657 - __name__ - INFO - [MainThread] - Starting search result with (173617) records
2023-09-19 10:04:48,781 - __name__ - INFO - [MainThread] - Query match count 6684
2023-09-19 10:04:48,788 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Query sequences with matches 'chembl' (6684) bitScore filter (False)
2023-09-19 10:04:57,883 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Completed searching chembl targets (status True) (cutoff=0.95) at 2023 09 19 10:04:57 (161.4171 seconds)
2023-09-19 10:06:25,748 - __name__ - INFO - [MainThread] - convertalis status is True
2023-09-19 10:06:31,521 - __name__ - INFO - [MainThread] - useTaxonomy flag (True)
2023-09-19 10:06:34,666 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy primary fetch status (True) using 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
2023-09-19 10:07:12,424 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy lengths name 2528571 node 2528676 merge 73969
2023-09-19 10:07:12,426 - __name__ - INFO - [MainThread] - Starting search result with (131516) records
2023-09-19 10:07:14,207 - __name__ - INFO - [MainThread] - Query match count 8840
2023-09-19 10:07:14,214 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Query sequences with matches 'pharos' (8840) bitScore filter (False)
2023-09-19 10:07:20,676 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Completed searching pharos targets (status True) (cutoff=0.95) at 2023 09 19 10:07:20 (142.7927 seconds)
2023-09-19 10:07:45,967 - __name__ - INFO - [MainThread] - convertalis status is True
2023-09-19 10:07:50,188 - __name__ - INFO - [MainThread] - useTaxonomy flag (True)
2023-09-19 10:07:53,175 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy primary fetch status (True) using 'https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz'
2023-09-19 10:08:28,294 - rcsb.utils.taxonomy.TaxonomyProvider - INFO - [MainThread] - Taxonomy lengths name 2528571 node 2528676 merge 73969
2023-09-19 10:08:28,295 - __name__ - INFO - [MainThread] - Starting search result with (89015) records
2023-09-19 10:08:29,210 - __name__ - INFO - [MainThread] - Query match count 2582
2023-09-19 10:08:29,250 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Query sequences with matches 'card' (2582) bitScore filter (True)
2023-09-19 10:08:32,958 - rcsb.workflow.targets.ProteinTargetSequenceWorkflow - INFO - [MainThread] - Completed searching card targets (status True) (cutoff=0.95) at 2023 09 19 10:08:32 (72.2820 seconds)
2023-09-19 10:08:32,959 - root - INFO - [MainThread] - Running buildFeatures...