Stage:
completed
Fetched:
23 Dec 09:38
Validated:
23 Dec 09:38
Deltas Created
23 Dec 09:39
Units Normalized:
23 Dec 09:54
Ancestry Built:
23 Dec 09:39
Nodes Matched:
23 Dec 09:54
Names Parsed:
23 Dec 09:39
New Models Stored:
23 Dec 09:39
Indexed:
23 Dec 09:54
Completed:
23 Dec 09:56
Time to Harvest:
less than a minute
Harvesting Log
(139 lines)
# Logfile created on 2019-12-23 09:38:51 -0500 by logger.rb/56815
[START] [2019-12-23 09:38:51] logged process
[START] [2019-12-23 09:38:51] create_harvest_instance
[STOP] [2019-12-23 09:38:51] create_harvest_instance
[START] [2019-12-23 09:38:51] fetch_files
[STOP] [2019-12-23 09:38:51] fetch_files
[START] [2019-12-23 09:38:51] validate_each_file
[STOP] [2019-12-23 09:38:52] validate_each_file
[START] [2019-12-23 09:38:52] convert_to_csv
[CMD] [2019-12-23 09:38:52] /usr/bin/sort /app/public/converted_csv/gslsl_refs_19346.csv > /app/public/converted_csv/gslsl_refs_19346.csv_sorted
[CMD] [2019-12-23 09:38:53] /usr/bin/sort /app/public/converted_csv/gslsl_nodes_19347.csv > /app/public/converted_csv/gslsl_nodes_19347.csv_sorted
[CMD] [2019-12-23 09:38:53] /usr/bin/sort /app/public/converted_csv/gslsl_occurrences_19348.csv > /app/public/converted_csv/gslsl_occurrences_19348.csv_sorted
[CMD] [2019-12-23 09:38:54] /usr/bin/sort /app/public/converted_csv/gslsl_measurements_19349.csv > /app/public/converted_csv/gslsl_measurements_19349.csv_sorted
[STOP] [2019-12-23 09:38:55] convert_to_csv
[START] [2019-12-23 09:38:55] calculate_delta
[CMD] [2019-12-23 09:38:55] echo "0a" > /app/public/diff/gslsl_refs_19346.diff
[CMD] [2019-12-23 09:38:55] tail -n +1 /app/public/converted_csv/gslsl_refs_19346.csv >> /app/public/diff/gslsl_refs_19346.diff
[CMD] [2019-12-23 09:38:56] echo "." >> /app/public/diff/gslsl_refs_19346.diff
[CMD] [2019-12-23 09:38:57] echo "0a" > /app/public/diff/gslsl_nodes_19347.diff
[CMD] [2019-12-23 09:38:57] tail -n +1 /app/public/converted_csv/gslsl_nodes_19347.csv >> /app/public/diff/gslsl_nodes_19347.diff
[CMD] [2019-12-23 09:38:58] echo "." >> /app/public/diff/gslsl_nodes_19347.diff
[CMD] [2019-12-23 09:38:59] echo "0a" > /app/public/diff/gslsl_occurrences_19348.diff
[CMD] [2019-12-23 09:38:59] tail -n +1 /app/public/converted_csv/gslsl_occurrences_19348.csv >> /app/public/diff/gslsl_occurrences_19348.diff
[CMD] [2019-12-23 09:39:00] echo "." >> /app/public/diff/gslsl_occurrences_19348.diff
[CMD] [2019-12-23 09:39:01] echo "0a" > /app/public/diff/gslsl_measurements_19349.diff
[CMD] [2019-12-23 09:39:01] tail -n +1 /app/public/converted_csv/gslsl_measurements_19349.csv >> /app/public/diff/gslsl_measurements_19349.diff
[CMD] [2019-12-23 09:39:02] echo "." >> /app/public/diff/gslsl_measurements_19349.diff
[STOP] [2019-12-23 09:39:03] calculate_delta
[START] [2019-12-23 09:39:03] parse_diff_and_store
[INFO] [2019-12-23 09:39:03] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 09:39:04] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 09:39:06] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 09:39:07] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 09:39:14] Storing 2 References
[INFO] [2019-12-23 09:39:14] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 09:39:14] Average Time: 0.0
[INFO] [2019-12-23 09:39:14] Total Time: 1s
[INFO] [2019-12-23 09:39:14] Storing 2822 ScientificNames
[INFO] [2019-12-23 09:39:14] Processing group of 2822 in 3 groups of 1000
[INFO] [2019-12-23 09:39:15] Average Time: 0.413
[INFO] [2019-12-23 09:39:15] Total Time: 2s
[INFO] [2019-12-23 09:39:15] Storing 2822 Nodes
[INFO] [2019-12-23 09:39:15] Processing group of 2822 in 3 groups of 1000
[INFO] [2019-12-23 09:39:16] Average Time: 0.36
[INFO] [2019-12-23 09:39:16] Total Time: 2s
[INFO] [2019-12-23 09:39:16] Storing 1234 Occurrences
[INFO] [2019-12-23 09:39:16] Processing group of 1234 in 2 groups of 1000
[INFO] [2019-12-23 09:39:16] Average Time: 0.085
[INFO] [2019-12-23 09:39:16] Total Time: 1s
[INFO] [2019-12-23 09:39:16] Storing 2468 TraitsReferences
[INFO] [2019-12-23 09:39:16] Processing group of 2468 in 3 groups of 1000
[INFO] [2019-12-23 09:39:17] Average Time: 0.097
[INFO] [2019-12-23 09:39:17] Total Time: 1s
[INFO] [2019-12-23 09:39:17] Storing 2468 Traits
[INFO] [2019-12-23 09:39:17] Processing group of 2468 in 3 groups of 1000
[INFO] [2019-12-23 09:39:18] Average Time: 0.333
[INFO] [2019-12-23 09:39:18] Total Time: 2s
[INFO] [2019-12-23 09:39:18] Storing 2467 MetaTraits
[INFO] [2019-12-23 09:39:18] Processing group of 2467 in 3 groups of 1000
[INFO] [2019-12-23 09:39:18] Average Time: 0.153
[INFO] [2019-12-23 09:39:18] Total Time: 1s
[STOP] [2019-12-23 09:39:18] parse_diff_and_store
[START] [2019-12-23 09:39:18] resolve_keys
[INFO] [2019-12-23 09:39:33] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 09:39:34] traits to occurrences...
[INFO] [2019-12-23 09:39:35] traits to nodes (through occurrences)...
[INFO] [2019-12-23 09:39:35] Traits to sex term...
[INFO] [2019-12-23 09:39:35] Traits to lifestage term...
[INFO] [2019-12-23 09:39:35] MetaTraits to traits...
[INFO] [2019-12-23 09:39:36] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 09:39:36] Assocs to occurrences...
[INFO] [2019-12-23 09:39:36] Assocs to nodes...
[INFO] [2019-12-23 09:39:36] Assoc to sex term...
[INFO] [2019-12-23 09:39:36] Assoc to lifestage term...
[STOP] [2019-12-23 09:39:36] resolve_keys
[START] [2019-12-23 09:39:36] hold_for_later_1
[STOP] [2019-12-23 09:39:36] hold_for_later_1
[START] [2019-12-23 09:39:36] hold_for_later_2
[STOP] [2019-12-23 09:39:36] hold_for_later_2
[START] [2019-12-23 09:39:36] resolve_missing_parents
[STOP] [2019-12-23 09:39:41] resolve_missing_parents
[START] [2019-12-23 09:39:41] rebuild_nodes
[START] [2019-12-23 09:39:41] Flattener#flatten
[START] [2019-12-23 09:39:41] Flattener#study_resource
[START] [2019-12-23 09:39:41] Flattener#build_ancestry
[STOP] [2019-12-23 09:39:41] Flattener#build_ancestry
[INFO] [2019-12-23 09:39:41] 2822 ancestry keys
[START] [2019-12-23 09:39:41] build_node_ancestors
[INFO] [2019-12-23 09:39:41] old ancestors deleted.
[STOP] [2019-12-23 09:39:42] build_node_ancestors
[START] [2019-12-23 09:39:43] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:39:44] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 09:39:44] Flattener#flatten
[STOP] [2019-12-23 09:39:44] rebuild_nodes
[START] [2019-12-23 09:39:44] resolve_missing_media_owners
[STOP] [2019-12-23 09:39:44] resolve_missing_media_owners
[START] [2019-12-23 09:39:44] sanitize_media_verbatims
[STOP] [2019-12-23 09:39:44] sanitize_media_verbatims
[START] [2019-12-23 09:39:44] queue_downloads
[STOP] [2019-12-23 09:39:44] queue_downloads
[START] [2019-12-23 09:39:44] parse_names
[WARN] [2019-12-23 09:39:44] I see 2822 names which still need to be parsed.
[STOP] [2019-12-23 09:39:47] parse_names
[START] [2019-12-23 09:39:47] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 09:39:47] denormalize_canonical_names_to_nodes
[START] [2019-12-23 09:39:47] match_nodes
[START] [2019-12-23 09:39:47] map_all_nodes_to_pages
[STOP] [2019-12-23 09:54:40] map_all_nodes_to_pages
[INFO] [2019-12-23 09:54:40] 156 Unmatched nodes (of 2822)! That's too many to output. First 10: Larus thayeri (#61958677); Tringa semipalmatus (#61960855); Limnodromus (#61958262); Philomachus (#61959066); Philomachus pugnax (#61959065); Anas americana (#61958222); Anas strepera (#61958238); Anas discors (#61958253); Anas clypeata (#61958285); Anas penelope (#61958480)
[START] [2019-12-23 09:54:40] update_nodes
[STOP] [2019-12-23 09:54:41] update_nodes
[STOP] [2019-12-23 09:54:41] match_nodes
[START] [2019-12-23 09:54:41] reindex_search
[STOP] [2019-12-23 09:54:50] reindex_search
[START] [2019-12-23 09:54:50] normalize_units
[STOP] [2019-12-23 09:54:50] normalize_units
[START] [2019-12-23 09:54:50] calculate_statistics
[STOP] [2019-12-23 09:54:50] calculate_statistics
[START] [2019-12-23 09:54:50] complete_harvest_instance
[START] [2019-12-23 09:54:50] overall_tsv_creation
[INFO] [2019-12-23 09:54:50] Processing group of 2822 in 1 batches of 10000
[INFO] [2019-12-23 09:55:48] 1234 Traits (unfiltered)...
[INFO] [2019-12-23 09:56:01] 1234 Traits (filtered)...
[INFO] [2019-12-23 09:56:01] 0 Associations (filtered)...
[INFO] [2019-12-23 09:56:40] 6169 metadata added.
[INFO] [2019-12-23 09:56:40] 0 metadata added.
[INFO] [2019-12-23 09:56:40] Average Time: 86.34
[INFO] [2019-12-23 09:56:40] Total Time: 1m51s
[STOP] [2019-12-23 09:56:40] overall_tsv_creation
[INFO] [2019-12-23 09:56:40] Done. Check your files:
[INFO] [2019-12-23 09:56:41] (2822 lines) /app/public/data/gslsl/publish_nodes.tsv
[INFO] [2019-12-23 09:56:42] (13794 lines) /app/public/data/gslsl/publish_node_ancestors.tsv
[INFO] [2019-12-23 09:56:42] (2822 lines) /app/public/data/gslsl/publish_scientific_names.tsv
[INFO] [2019-12-23 09:56:43] (1235 lines) /app/public/data/gslsl/publish_traits.tsv
[INFO] [2019-12-23 09:56:44] (6170 lines) /app/public/data/gslsl/publish_metadata.tsv
[STOP] [2019-12-23 09:56:44] complete_harvest_instance
[START] [2019-12-23 09:56:44] completed
[STOP] [2019-12-23 09:56:44] completed
[STOP] [2019-12-23 09:56:44] logged process, took 1073.14
Latest Process