Harvest for Makassar Strait Species List Created 23 Dec 18:12

Stage: completed
Fetched: 23 Dec 18:12
Validated: 23 Dec 18:12
Deltas Created 23 Dec 18:12
Units Normalized: 23 Dec 18:25
Ancestry Built: 23 Dec 18:13
Nodes Matched: 23 Dec 18:24
Names Parsed: 23 Dec 18:14
New Models Stored: 23 Dec 18:13
Indexed: 23 Dec 18:25
Completed: 23 Dec 18:27
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-12-23 18:12:43 -0500 by logger.rb/56815
[START] [2019-12-23 18:12:43] logged process
[START] [2019-12-23 18:12:43] create_harvest_instance
[STOP] [2019-12-23 18:12:44] create_harvest_instance
[START] [2019-12-23 18:12:44] fetch_files
[STOP] [2019-12-23 18:12:44] fetch_files
[START] [2019-12-23 18:12:44] validate_each_file
[STOP] [2019-12-23 18:12:45] validate_each_file
[START] [2019-12-23 18:12:45] convert_to_csv
[CMD] [2019-12-23 18:12:45] /usr/bin/sort /app/public/converted_csv/makassar_strait__refs_19466.csv > /app/public/converted_csv/makassar_strait__refs_19466.csv_sorted
[CMD] [2019-12-23 18:12:45] /usr/bin/sort /app/public/converted_csv/makassar_strait__nodes_19467.csv > /app/public/converted_csv/makassar_strait__nodes_19467.csv_sorted
[CMD] [2019-12-23 18:12:46] /usr/bin/sort /app/public/converted_csv/makassar_strait__occurrences_19468.csv > /app/public/converted_csv/makassar_strait__occurrences_19468.csv_sorted
[CMD] [2019-12-23 18:12:47] /usr/bin/sort /app/public/converted_csv/makassar_strait__measurements_19469.csv > /app/public/converted_csv/makassar_strait__measurements_19469.csv_sorted
[STOP] [2019-12-23 18:12:47] convert_to_csv
[START] [2019-12-23 18:12:47] calculate_delta
[CMD] [2019-12-23 18:12:47] echo "0a" > /app/public/diff/makassar_strait__refs_19466.diff
[CMD] [2019-12-23 18:12:48] tail -n +1 /app/public/converted_csv/makassar_strait__refs_19466.csv >> /app/public/diff/makassar_strait__refs_19466.diff
[CMD] [2019-12-23 18:12:48] echo "." >> /app/public/diff/makassar_strait__refs_19466.diff
[CMD] [2019-12-23 18:12:49] echo "0a" > /app/public/diff/makassar_strait__nodes_19467.diff
[CMD] [2019-12-23 18:12:50] tail -n +1 /app/public/converted_csv/makassar_strait__nodes_19467.csv >> /app/public/diff/makassar_strait__nodes_19467.diff
[CMD] [2019-12-23 18:12:50] echo "." >> /app/public/diff/makassar_strait__nodes_19467.diff
[CMD] [2019-12-23 18:12:51] echo "0a" > /app/public/diff/makassar_strait__occurrences_19468.diff
[CMD] [2019-12-23 18:12:52] tail -n +1 /app/public/converted_csv/makassar_strait__occurrences_19468.csv >> /app/public/diff/makassar_strait__occurrences_19468.diff
[CMD] [2019-12-23 18:12:52] echo "." >> /app/public/diff/makassar_strait__occurrences_19468.diff
[CMD] [2019-12-23 18:12:53] echo "0a" > /app/public/diff/makassar_strait__measurements_19469.diff
[CMD] [2019-12-23 18:12:53] tail -n +1 /app/public/converted_csv/makassar_strait__measurements_19469.csv >> /app/public/diff/makassar_strait__measurements_19469.diff
[CMD] [2019-12-23 18:12:54] echo "." >> /app/public/diff/makassar_strait__measurements_19469.diff
[STOP] [2019-12-23 18:12:55] calculate_delta
[START] [2019-12-23 18:12:55] parse_diff_and_store
[INFO] [2019-12-23 18:12:55] Loading refs diff file into memory (true lines)...
[INFO] [2019-12-23 18:12:56] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-23 18:12:58] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-12-23 18:12:59] Loading measurements diff file into memory (true lines)...
[INFO] [2019-12-23 18:13:10] Storing 2 References
[INFO] [2019-12-23 18:13:10] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-23 18:13:10] Average Time: 0.0
[INFO] [2019-12-23 18:13:10] Total Time: 1s
[INFO] [2019-12-23 18:13:10] Storing 3989 ScientificNames
[INFO] [2019-12-23 18:13:10] Processing group of 3989 in 4 groups of 1000
[INFO] [2019-12-23 18:13:12] Average Time: 0.428
[INFO] [2019-12-23 18:13:12] Total Time: 2s
[INFO] [2019-12-23 18:13:12] Storing 3989 Nodes
[INFO] [2019-12-23 18:13:12] Processing group of 3989 in 4 groups of 1000
[INFO] [2019-12-23 18:13:13] Average Time: 0.313
[INFO] [2019-12-23 18:13:13] Total Time: 2s
[INFO] [2019-12-23 18:13:13] Storing 2004 Occurrences
[INFO] [2019-12-23 18:13:13] Processing group of 2004 in 3 groups of 1000
[INFO] [2019-12-23 18:13:13] Average Time: 0.077
[INFO] [2019-12-23 18:13:13] Total Time: 1s
[INFO] [2019-12-23 18:13:13] Storing 4008 TraitsReferences
[INFO] [2019-12-23 18:13:13] Processing group of 4008 in 5 groups of 1000
[INFO] [2019-12-23 18:13:14] Average Time: 0.072
[INFO] [2019-12-23 18:13:14] Total Time: 1s
[INFO] [2019-12-23 18:13:14] Storing 4008 Traits
[INFO] [2019-12-23 18:13:14] Processing group of 4008 in 5 groups of 1000
[INFO] [2019-12-23 18:13:15] Average Time: 0.296
[INFO] [2019-12-23 18:13:15] Total Time: 2s
[INFO] [2019-12-23 18:13:15] Storing 4008 MetaTraits
[INFO] [2019-12-23 18:13:15] Processing group of 4008 in 5 groups of 1000
[INFO] [2019-12-23 18:13:16] Average Time: 0.12
[INFO] [2019-12-23 18:13:16] Total Time: 1s
[STOP] [2019-12-23 18:13:16] parse_diff_and_store
[START] [2019-12-23 18:13:16] resolve_keys
[INFO] [2019-12-23 18:13:40] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-23 18:13:42] traits to occurrences...
[INFO] [2019-12-23 18:13:43] traits to nodes (through occurrences)...
[INFO] [2019-12-23 18:13:43] Traits to sex term...
[INFO] [2019-12-23 18:13:43] Traits to lifestage term...
[INFO] [2019-12-23 18:13:44] MetaTraits to traits...
[INFO] [2019-12-23 18:13:44] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-23 18:13:45] Assocs to occurrences...
[INFO] [2019-12-23 18:13:45] Assocs to nodes...
[INFO] [2019-12-23 18:13:45] Assoc to sex term...
[INFO] [2019-12-23 18:13:45] Assoc to lifestage term...
[STOP] [2019-12-23 18:13:45] resolve_keys
[START] [2019-12-23 18:13:45] hold_for_later_1
[STOP] [2019-12-23 18:13:45] hold_for_later_1
[START] [2019-12-23 18:13:45] hold_for_later_2
[STOP] [2019-12-23 18:13:45] hold_for_later_2
[START] [2019-12-23 18:13:45] resolve_missing_parents
[STOP] [2019-12-23 18:13:53] resolve_missing_parents
[START] [2019-12-23 18:13:53] rebuild_nodes
[START] [2019-12-23 18:13:53] Flattener#flatten
[START] [2019-12-23 18:13:53] Flattener#study_resource
[START] [2019-12-23 18:13:53] Flattener#build_ancestry
[STOP] [2019-12-23 18:13:53] Flattener#build_ancestry
[INFO] [2019-12-23 18:13:53] 3989 ancestry keys
[START] [2019-12-23 18:13:53] build_node_ancestors
[INFO] [2019-12-23 18:13:53] old ancestors deleted.
[STOP] [2019-12-23 18:13:54] build_node_ancestors
[START] [2019-12-23 18:13:56] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 18:13:56] Flattener#propagate_ancestor_ids
[STOP] [2019-12-23 18:13:56] Flattener#flatten
[STOP] [2019-12-23 18:13:56] rebuild_nodes
[START] [2019-12-23 18:13:56] resolve_missing_media_owners
[STOP] [2019-12-23 18:13:56] resolve_missing_media_owners
[START] [2019-12-23 18:13:56] sanitize_media_verbatims
[STOP] [2019-12-23 18:13:56] sanitize_media_verbatims
[START] [2019-12-23 18:13:56] queue_downloads
[STOP] [2019-12-23 18:13:56] queue_downloads
[START] [2019-12-23 18:13:56] parse_names
[WARN] [2019-12-23 18:13:56] I see 3989 names which still need to be parsed.
[STOP] [2019-12-23 18:14:00] parse_names
[START] [2019-12-23 18:14:00] denormalize_canonical_names_to_nodes
[STOP] [2019-12-23 18:14:00] denormalize_canonical_names_to_nodes
[START] [2019-12-23 18:14:00] match_nodes
[START] [2019-12-23 18:14:00] map_all_nodes_to_pages
[STOP] [2019-12-23 18:24:52] map_all_nodes_to_pages
[INFO] [2019-12-23 18:24:52] 200 Unmatched nodes (of 3989)! That's too many to output. First 10: Acropora haimei (#62102810); Acropora lutkeni (#62105531); Caulastrea (#62103010); Porites tumida (#62103260); Acrhelia (#62103230); Pectiniidae (#62102803); Euphyllidae (#62102887); Mussidae (#62102922); Symphyllia (#62102949); Trachyphylliidae (#62103237)
[START] [2019-12-23 18:24:52] update_nodes
[STOP] [2019-12-23 18:24:53] update_nodes
[STOP] [2019-12-23 18:24:53] match_nodes
[START] [2019-12-23 18:24:53] reindex_search
[STOP] [2019-12-23 18:25:02] reindex_search
[START] [2019-12-23 18:25:02] normalize_units
[STOP] [2019-12-23 18:25:02] normalize_units
[START] [2019-12-23 18:25:02] calculate_statistics
[STOP] [2019-12-23 18:25:03] calculate_statistics
[START] [2019-12-23 18:25:03] complete_harvest_instance
[START] [2019-12-23 18:25:03] overall_tsv_creation
[INFO] [2019-12-23 18:25:03] Processing group of 3989 in 1 batches of 10000
[INFO] [2019-12-23 18:26:08] 2004 Traits (unfiltered)...
[INFO] [2019-12-23 18:26:22] 2004 Traits (filtered)...
[INFO] [2019-12-23 18:26:22] 0 Associations (filtered)...
[INFO] [2019-12-23 18:27:05] 10020 metadata added.
[INFO] [2019-12-23 18:27:05] 0 metadata added.
[INFO] [2019-12-23 18:27:06] Average Time: 96.71
[INFO] [2019-12-23 18:27:06] Total Time: 2m4s
[STOP] [2019-12-23 18:27:06] overall_tsv_creation
[INFO] [2019-12-23 18:27:06] Done. Check your files:
[INFO] [2019-12-23 18:27:06] (3989 lines) /app/public/data/makassar_strait_/publish_nodes.tsv
[INFO] [2019-12-23 18:27:07] (20129 lines) /app/public/data/makassar_strait_/publish_node_ancestors.tsv
[INFO] [2019-12-23 18:27:07] (3989 lines) /app/public/data/makassar_strait_/publish_scientific_names.tsv
[INFO] [2019-12-23 18:27:08] (2005 lines) /app/public/data/makassar_strait_/publish_traits.tsv
[INFO] [2019-12-23 18:27:09] (10021 lines) /app/public/data/makassar_strait_/publish_metadata.tsv
[STOP] [2019-12-23 18:27:09] complete_harvest_instance
[START] [2019-12-23 18:27:09] completed
[STOP] [2019-12-23 18:27:09] completed
[STOP] [2019-12-23 18:27:09] logged process, took 866.1
Latest Process

23 Dec 18:12 EXITED currently processing 0