Harvest for Eastern China Sea Species List Created 23 Dec 00:48

Stage: completed
Fetched: 23 Dec 00:48
Validated: 23 Dec 00:48
Deltas Created 23 Dec 00:48
Units Normalized: 23 Dec 01:20
Ancestry Built: 23 Dec 00:50
Nodes Matched: 23 Dec 01:19
Names Parsed: 23 Dec 00:50
New Models Stored: 23 Dec 00:48
Indexed: 23 Dec 01:20
Completed: 23 Dec 01:22
Time to Harvest: 1 minute
Harvesting Log

(149 lines)
# Logfile created on 2019-12-23 00:48:16 -0500 by logger.rb/56815
[START] [2019-12-23 00:48:16] logged process
[START] [2019-12-23 00:48:16] create_harvest_instance
[STOP] [2019-12-23 00:48:18] create_harvest_instance
[START] [2019-12-23 00:48:18] fetch_files
[STOP] [2019-12-23 00:48:18] fetch_files
[START] [2019-12-23 00:48:18] validate_each_file
[STOP] [2019-12-23 00:48:19] validate_each_file
[START] [2019-12-23 00:48:19] convert_to_csv
[CMD] [2019-12-23 00:48:19] /usr/bin/sort /app/public/converted_csv/ecssl_refs_19218.csv > /app/public/converted_csv/ecssl_refs_19218.csv_sorted
[CMD] [2019-12-23 00:48:19] /usr/bin/sort /app/public/converted_csv/ecssl_nodes_19219.csv > /app/public/converted_csv/ecssl_nodes_19219.csv_sorted
[CMD] [2019-12-23 00:48:19] /usr/bin/sort /app/public/converted_csv/ecssl_occurrences_19220.csv > /app/public/converted_csv/ecssl_occurrences_19220.csv_sorted
[CMD] [2019-12-23 00:48:19] /usr/bin/sort /app/public/converted_csv/ecssl_measurements_19221.csv > /app/public/converted_csv/ecssl_measurements_19221.csv_sorted
[STOP] [2019-12-23 00:48:19] convert_to_csv
[START] [2019-12-23 00:48:19] calculate_delta
[CMD] [2019-12-23 00:48:19] echo "0a" > /app/public/diff/ecssl_refs_19218.diff
[CMD] [2019-12-23 00:48:19] tail -n +1 /app/public/converted_csv/ecssl_refs_19218.csv >> /app/public/diff/ecssl_refs_19218.diff
[CMD] [2019-12-23 00:48:19] echo "." >> /app/public/diff/ecssl_refs_19218.diff
[CMD] [2019-12-23 00:48:20] echo "0a" > /app/public/diff/ecssl_nodes_19219.diff
[CMD] [2019-12-23 00:48:20] tail -n +1 /app/public/converted_csv/ecssl_nodes_19219.csv >> /app/public/diff/ecssl_nodes_19219.diff
[CMD] [2019-12-23 00:48:20] echo "." >> /app/public/diff/ecssl_nodes_19219.diff
[CMD] [2019-12-23 00:48:20] echo "0a" > /app/public/diff/ecssl_occurrences_19220.diff
[CMD] [2019-12-23 00:48:20] tail -n +1 /app/public/converted_csv/ecssl_occurrences_19220.csv >> /app/public/diff/ecssl_occurrences_19220.diff
[CMD] [2019-12-23 00:48:20] echo "." >> /app/public/diff/ecssl_occurrences_19220.diff
[CMD] [2019-12-23 00:48:20] echo "0a" > /app/public/diff/ecssl_measurements_19221.diff
[CMD] [2019-12-23 00:48:20] tail -n +1 /app/public/converted_csv/ecssl_measurements_19221.csv >> /app/public/diff/ecssl_measurements_19221.diff
[CMD] [2019-12-23 00:48:20] echo "." >> /app/public/diff/ecssl_measurements_19221.diff
[STOP] [2019-12-23 00:48:20] calculate_delta
[START] [2019-12-23 00:48:20] parse_diff_and_store
[INFO] [2019-12-23 00:48:20] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 00:48:20] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 00:48:23] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 00:48:24] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 00:48:48] Storing 2 References
[INFO] [2019-12-23 00:48:48] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 00:48:48] Average Time: 0.0
[INFO] [2019-12-23 00:48:48] Total Time: 1s
[INFO] [2019-12-23 00:48:48] Storing 7748 ScientificNames
[INFO] [2019-12-23 00:48:48] Processing group of 7748 in 8 groups of 1000
[INFO] [2019-12-23 00:48:51] Average Time: 0.411
[INFO] [2019-12-23 00:48:51] Total Time: 4s
[INFO] [2019-12-23 00:48:51] last 3 / first 3: 0.82
[INFO] [2019-12-23 00:48:51] Std.Dev: 0.07071067811865475; Max: 0.52
[INFO] [2019-12-23 00:48:51] Storing 7748 Nodes
[INFO] [2019-12-23 00:48:51] Processing group of 7748 in 8 groups of 1000
[INFO] [2019-12-23 00:48:54] Average Time: 0.326
[INFO] [2019-12-23 00:48:54] Total Time: 3s
[INFO] [2019-12-23 00:48:54] last 3 / first 3: 0.9
[INFO] [2019-12-23 00:48:54] Std.Dev: 0.03162277660168379; Max: 0.37
[INFO] [2019-12-23 00:48:54] Storing 4113 Occurrences
[INFO] [2019-12-23 00:48:54] Processing group of 4113 in 5 groups of 1000
[INFO] [2019-12-23 00:48:54] Average Time: 0.098
[INFO] [2019-12-23 00:48:54] Total Time: 1s
[INFO] [2019-12-23 00:48:54] Storing 8226 TraitsReferences
[INFO] [2019-12-23 00:48:54] Processing group of 8226 in 9 groups of 1000
[INFO] [2019-12-23 00:48:55] Average Time: 0.12
[INFO] [2019-12-23 00:48:55] Total Time: 2s
[INFO] [2019-12-23 00:48:55] last 3 / first 3: 0.34
[INFO] [2019-12-23 00:48:55] Std.Dev: 0.06324555320336758; Max: 0.21
[INFO] [2019-12-23 00:48:55] Storing 8226 Traits
[INFO] [2019-12-23 00:48:55] Processing group of 8226 in 9 groups of 1000
[INFO] [2019-12-23 00:48:58] Average Time: 0.308
[INFO] [2019-12-23 00:48:58] Total Time: 3s
[INFO] [2019-12-23 00:48:58] last 3 / first 3: 0.63
[INFO] [2019-12-23 00:48:58] Std.Dev: 0.1; Max: 0.46
[INFO] [2019-12-23 00:48:58] Storing 8225 MetaTraits
[INFO] [2019-12-23 00:48:58] Processing group of 8225 in 9 groups of 1000
[INFO] [2019-12-23 00:48:59] Average Time: 0.124
[INFO] [2019-12-23 00:48:59] Total Time: 2s
[INFO] [2019-12-23 00:48:59] last 3 / first 3: 0.64
[INFO] [2019-12-23 00:48:59] Std.Dev: 0.044721359549995794; Max: 0.17
[STOP] [2019-12-23 00:48:59] parse_diff_and_store
[START] [2019-12-23 00:48:59] resolve_keys
[INFO] [2019-12-23 00:49:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 00:49:32] traits to occurrences...
[INFO] [2019-12-23 00:49:34] traits to nodes (through occurrences)...
[INFO] [2019-12-23 00:49:34] Traits to sex term...
[INFO] [2019-12-23 00:49:36] Traits to lifestage term...
[INFO] [2019-12-23 00:49:38] MetaTraits to traits...
[INFO] [2019-12-23 00:49:38] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 00:49:39] Assocs to occurrences...
[INFO] [2019-12-23 00:49:39] Assocs to nodes...
[INFO] [2019-12-23 00:49:39] Assoc to sex term...
[INFO] [2019-12-23 00:49:39] Assoc to lifestage term...
[STOP] [2019-12-23 00:49:39] resolve_keys
[START] [2019-12-23 00:49:39] hold_for_later_1
[STOP] [2019-12-23 00:49:39] hold_for_later_1
[START] [2019-12-23 00:49:39] hold_for_later_2
[STOP] [2019-12-23 00:49:39] hold_for_later_2
[START] [2019-12-23 00:49:39] resolve_missing_parents
[STOP] [2019-12-23 00:49:55] resolve_missing_parents
[START] [2019-12-23 00:49:55] rebuild_nodes
[START] [2019-12-23 00:49:55] Flattener#flatten
[START] [2019-12-23 00:49:55] Flattener#study_resource
[START] [2019-12-23 00:49:55] Flattener#build_ancestry
[STOP] [2019-12-23 00:49:56] Flattener#build_ancestry
[INFO] [2019-12-23 00:49:56] 7748 ancestry keys
[START] [2019-12-23 00:49:56] build_node_ancestors
[INFO] [2019-12-23 00:49:56] old ancestors deleted.
[STOP] [2019-12-23 00:49:59] build_node_ancestors
[START] [2019-12-23 00:50:03] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:50:04] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 00:50:04] Flattener#flatten
[STOP] [2019-12-23 00:50:04] rebuild_nodes
[START] [2019-12-23 00:50:04] resolve_missing_media_owners
[STOP] [2019-12-23 00:50:04] resolve_missing_media_owners
[START] [2019-12-23 00:50:04] sanitize_media_verbatims
[STOP] [2019-12-23 00:50:04] sanitize_media_verbatims
[START] [2019-12-23 00:50:04] queue_downloads
[STOP] [2019-12-23 00:50:04] queue_downloads
[START] [2019-12-23 00:50:04] parse_names
[WARN] [2019-12-23 00:50:04] I see 7748 names which still need to be parsed.
[STOP] [2019-12-23 00:50:11] parse_names
[START] [2019-12-23 00:50:11] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 00:50:11] denormalize_canonical_names_to_nodes
[START] [2019-12-23 00:50:11] match_nodes
[START] [2019-12-23 00:50:11] map_all_nodes_to_pages
[STOP] [2019-12-23 01:19:53] map_all_nodes_to_pages
[INFO] [2019-12-23 01:19:53] 340 Unmatched nodes (of 7748)! That's too many to output. First 10: Thalassionematales (#61859872); Hemiaulus indicus (#61862145); Streptothecaceae (#61861077); Streptotheca (#61861076); Streptotheca thamensis (#61861075); Corethron pelagicum (#61861011); Leptocylindrus mediterraneus (#61860017); Tropidoneis lepidoptera (#61867093); Plagiotropis lepidoptera (#61867298); Chaetoceros distans (#61860776)
[START] [2019-12-23 01:19:53] update_nodes
[STOP] [2019-12-23 01:19:56] update_nodes
[STOP] [2019-12-23 01:19:56] match_nodes
[START] [2019-12-23 01:19:56] reindex_search
[STOP] [2019-12-23 01:20:17] reindex_search
[START] [2019-12-23 01:20:17] normalize_units
[STOP] [2019-12-23 01:20:17] normalize_units
[START] [2019-12-23 01:20:17] calculate_statistics
[STOP] [2019-12-23 01:20:17] calculate_statistics
[START] [2019-12-23 01:20:17] complete_harvest_instance
[START] [2019-12-23 01:20:17] overall_tsv_creation
[INFO] [2019-12-23 01:20:17] Processing group of 7748 in 1 batches of 10000
[INFO] [2019-12-23 01:21:40] 4113 Traits (unfiltered)...
[INFO] [2019-12-23 01:21:54] 4113 Traits (filtered)...
[INFO] [2019-12-23 01:21:54] 0 Associations (filtered)...
[INFO] [2019-12-23 01:22:41] 20564 metadata added.
[INFO] [2019-12-23 01:22:41] 0 metadata added.
[INFO] [2019-12-23 01:22:41] Average Time: 115.82
[INFO] [2019-12-23 01:22:41] Total Time: 2m24s
[STOP] [2019-12-23 01:22:41] overall_tsv_creation
[INFO] [2019-12-23 01:22:41] Done. Check your files:
[INFO] [2019-12-23 01:22:41] (7748 lines) /app/public/data/ecssl/publish_nodes.tsv
[INFO] [2019-12-23 01:22:41] (39849 lines) /app/public/data/ecssl/publish_node_ancestors.tsv
[INFO] [2019-12-23 01:22:42] (7748 lines) /app/public/data/ecssl/publish_scientific_names.tsv
[INFO] [2019-12-23 01:22:42] (4114 lines) /app/public/data/ecssl/publish_traits.tsv
[INFO] [2019-12-23 01:22:42] (20565 lines) /app/public/data/ecssl/publish_metadata.tsv
[STOP] [2019-12-23 01:22:42] complete_harvest_instance
[START] [2019-12-23 01:22:42] completed
[STOP] [2019-12-23 01:22:42] completed
[STOP] [2019-12-23 01:22:42] logged process, took 2065.81
Latest Process

23 Dec 00:48 EXITED currently processing 0