Stage:
completed
Fetched:
17 Jul 15:01
Validated:
17 Jul 15:01
Deltas Created
17 Jul 15:01
Units Normalized:
17 Jul 15:07
Ancestry Built:
17 Jul 15:02
Nodes Matched:
17 Jul 15:07
Names Parsed:
17 Jul 15:03
New Models Stored:
17 Jul 15:02
Indexed:
17 Jul 15:07
Completed:
17 Jul 15:09
Time to Harvest:
less than a minute
Harvesting Log
(110 lines)
# Logfile created on 2019-07-17 15:01:43 -0400 by logger.rb/56815
[START] [2019-07-17 15:01:43] logged process
[START] [2019-07-17 15:01:43] create_harvest_instance
[STOP] [2019-07-17 15:01:44] create_harvest_instance
[START] [2019-07-17 15:01:44] fetch_files
[STOP] [2019-07-17 15:01:44] fetch_files
[START] [2019-07-17 15:01:44] validate_each_file
[STOP] [2019-07-17 15:01:46] validate_each_file
[START] [2019-07-17 15:01:46] convert_to_csv
[CMD] [2019-07-17 15:01:46] /usr/bin/sort /app/public/converted_csv/fdffas_refs_14258.csv > /app/public/converted_csv/fdffas_refs_14258.csv_sorted
[CMD] [2019-07-17 15:01:47] /usr/bin/sort /app/public/converted_csv/fdffas_nodes_14259.csv > /app/public/converted_csv/fdffas_nodes_14259.csv_sorted
[STOP] [2019-07-17 15:01:49] convert_to_csv
[START] [2019-07-17 15:01:49] calculate_delta
[CMD] [2019-07-17 15:01:49] echo "0a" > /app/public/diff/fdffas_refs_14258.diff
[CMD] [2019-07-17 15:01:51] tail -n +1 /app/public/converted_csv/fdffas_refs_14258.csv >> /app/public/diff/fdffas_refs_14258.diff
[CMD] [2019-07-17 15:01:52] echo "." >> /app/public/diff/fdffas_refs_14258.diff
[CMD] [2019-07-17 15:01:54] echo "0a" > /app/public/diff/fdffas_nodes_14259.diff
[CMD] [2019-07-17 15:01:56] tail -n +1 /app/public/converted_csv/fdffas_nodes_14259.csv >> /app/public/diff/fdffas_nodes_14259.diff
[CMD] [2019-07-17 15:01:57] echo "." >> /app/public/diff/fdffas_nodes_14259.diff
[STOP] [2019-07-17 15:01:59] calculate_delta
[START] [2019-07-17 15:01:59] parse_diff_and_store
[INFO] [2019-07-17 15:02:00] Loading refs diff file into memory (true lines)...
[INFO] [2019-07-17 15:02:03] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-17 15:02:14] Storing 4775 References
[INFO] [2019-07-17 15:02:14] Processing group of 4775 in 5 groups of 1000
[INFO] [2019-07-17 15:02:15] Average Time: 0.264
[INFO] [2019-07-17 15:02:15] Total Time: 2s
[INFO] [2019-07-17 15:02:15] Storing 31030 ScientificNames
[INFO] [2019-07-17 15:02:15] Processing group of 31030 in 32 groups of 1000
[INFO] [2019-07-17 15:02:27] Average Time: 0.369
[INFO] [2019-07-17 15:02:27] Total Time: 12s
[INFO] [2019-07-17 15:02:27] last 3 / first 3: 0.66
[INFO] [2019-07-17 15:02:27] Std.Dev: 0.08944271909999159; Max: 0.69
[INFO] [2019-07-17 15:02:27] Storing 8733 Nodes
[INFO] [2019-07-17 15:02:27] Processing group of 8733 in 9 groups of 1000
[INFO] [2019-07-17 15:02:30] Average Time: 0.289
[INFO] [2019-07-17 15:02:30] Total Time: 3s
[INFO] [2019-07-17 15:02:30] last 3 / first 3: 0.88
[INFO] [2019-07-17 15:02:30] Std.Dev: 0.03162277660168379; Max: 0.33
[STOP] [2019-07-17 15:02:30] parse_diff_and_store
[START] [2019-07-17 15:02:30] resolve_keys
[INFO] [2019-07-17 15:02:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-17 15:02:36] traits to occurrences...
[INFO] [2019-07-17 15:02:36] traits to nodes (through occurrences)...
[INFO] [2019-07-17 15:02:36] Traits to sex term...
[INFO] [2019-07-17 15:02:36] Traits to lifestage term...
[INFO] [2019-07-17 15:02:36] MetaTraits to traits...
[INFO] [2019-07-17 15:02:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-17 15:02:36] Assocs to occurrences...
[INFO] [2019-07-17 15:02:36] Assocs to nodes...
[INFO] [2019-07-17 15:02:36] Assoc to sex term...
[INFO] [2019-07-17 15:02:36] Assoc to lifestage term...
[STOP] [2019-07-17 15:02:36] resolve_keys
[START] [2019-07-17 15:02:36] hold_for_later_1
[STOP] [2019-07-17 15:02:36] hold_for_later_1
[START] [2019-07-17 15:02:36] hold_for_later_2
[STOP] [2019-07-17 15:02:36] hold_for_later_2
[START] [2019-07-17 15:02:36] resolve_missing_parents
[STOP] [2019-07-17 15:02:36] resolve_missing_parents
[START] [2019-07-17 15:02:36] rebuild_nodes
[START] [2019-07-17 15:02:36] Flattener#flatten
[START] [2019-07-17 15:02:36] Flattener#study_resource
[START] [2019-07-17 15:02:36] Flattener#build_ancestry
[STOP] [2019-07-17 15:02:36] Flattener#build_ancestry
[INFO] [2019-07-17 15:02:36] 8733 ancestry keys
[START] [2019-07-17 15:02:36] build_node_ancestors
[INFO] [2019-07-17 15:02:36] old ancestors deleted.
[STOP] [2019-07-17 15:02:39] build_node_ancestors
[START] [2019-07-17 15:02:42] Flattener#propagate_ancestor_ids
[STOP] [2019-07-17 15:02:43] Flattener#propagate_ancestor_ids
[STOP] [2019-07-17 15:02:43] Flattener#flatten
[STOP] [2019-07-17 15:02:43] rebuild_nodes
[START] [2019-07-17 15:02:43] resolve_missing_media_owners
[STOP] [2019-07-17 15:02:43] resolve_missing_media_owners
[START] [2019-07-17 15:02:43] sanitize_media_verbatims
[STOP] [2019-07-17 15:02:43] sanitize_media_verbatims
[START] [2019-07-17 15:02:43] queue_downloads
[STOP] [2019-07-17 15:02:43] queue_downloads
[START] [2019-07-17 15:02:43] parse_names
[WARN] [2019-07-17 15:02:43] I see 31030 names which still need to be parsed.
[STOP] [2019-07-17 15:03:10] parse_names
[START] [2019-07-17 15:03:10] denormalize_canonical_names_to_nodes
[STOP] [2019-07-17 15:03:10] denormalize_canonical_names_to_nodes
[START] [2019-07-17 15:03:10] match_nodes
[START] [2019-07-17 15:03:10] map_all_nodes_to_pages
[STOP] [2019-07-17 15:07:24] map_all_nodes_to_pages
[INFO] [2019-07-17 15:07:24] 197 Unmatched nodes (of 8733)! That's too many to output. First 10: Syrrhophus (#44586877); Syrrhophus (#44587513); Tomopterna branchi (#44589641); Diasporus amirae (#44583997); Blommersia transmarina (#44589041); Anomaloglossus mitaraka (#44589268); Colostethus dunni (#44585338); Allobates carajas (#44583437); "Colostethus" poecilonotus Rivero, 1991 (#44582904); Oophaga andresi (#44584983)
[START] [2019-07-17 15:07:24] update_nodes
[STOP] [2019-07-17 15:07:27] update_nodes
[STOP] [2019-07-17 15:07:27] match_nodes
[START] [2019-07-17 15:07:28] reindex_search
[STOP] [2019-07-17 15:07:49] reindex_search
[START] [2019-07-17 15:07:50] normalize_units
[STOP] [2019-07-17 15:07:50] normalize_units
[START] [2019-07-17 15:07:50] calculate_statistics
[STOP] [2019-07-17 15:07:50] calculate_statistics
[START] [2019-07-17 15:07:50] complete_harvest_instance
[START] [2019-07-17 15:07:50] overall_tsv_creation
[INFO] [2019-07-17 15:07:50] Processing group of 8733 in 1 batches of 10000
[INFO] [2019-07-17 15:09:48] Average Time: 73.08
[INFO] [2019-07-17 15:09:48] Total Time: 1m59s
[STOP] [2019-07-17 15:09:48] overall_tsv_creation
[INFO] [2019-07-17 15:09:48] Done. Check your files:
[INFO] [2019-07-17 15:09:50] (8733 lines) /app/public/data/fdffas/publish_nodes.tsv
[INFO] [2019-07-17 15:09:52] (38174 lines) /app/public/data/fdffas/publish_node_ancestors.tsv
[INFO] [2019-07-17 15:09:53] (31027 lines) /app/public/data/fdffas/publish_scientific_names.tsv
[STOP] [2019-07-17 15:09:53] complete_harvest_instance
[START] [2019-07-17 15:09:53] completed
[STOP] [2019-07-17 15:09:53] completed
[STOP] [2019-07-17 15:09:53] logged process, took 490.15
Latest Process