Harvest for Antigua and Barbuda Species List Created 02 Oct 01:03

Stage: completed
Fetched: 02 Oct 01:03
Validated: 02 Oct 01:03
Deltas Created 02 Oct 01:04
Units Normalized: 02 Oct 01:05
Ancestry Built: 02 Oct 01:04
Nodes Matched: 02 Oct 01:05
Names Parsed: 02 Oct 01:04
New Models Stored: 02 Oct 01:04
Indexed: 02 Oct 01:05
Completed: 02 Oct 01:07
Time to Harvest: less than a minute

Harvesting Log (most recent first)

# Logfile created on 2019-10-02 01:03:55 -0400 by logger.rb/56815
[START] [2019-10-02 01:03:55] logged process
[START] [2019-10-02 01:03:55] create_harvest_instance
[STOP] [2019-10-02 01:03:56] create_harvest_instance
[START] [2019-10-02 01:03:56] fetch_files
[STOP] [2019-10-02 01:03:56] fetch_files
[START] [2019-10-02 01:03:56] validate_each_file
[STOP] [2019-10-02 01:03:56] validate_each_file
[START] [2019-10-02 01:03:56] convert_to_csv
[CMD] [2019-10-02 01:03:56] /usr/bin/sort /app/public/converted_csv/antigua_barbuda__refs_14874.csv > /app/public/converted_csv/antigua_barbuda__refs_14874.csv_sorted
[CMD] [2019-10-02 01:03:57] /usr/bin/sort /app/public/converted_csv/antigua_barbuda__nodes_14875.csv > /app/public/converted_csv/antigua_barbuda__nodes_14875.csv_sorted
[CMD] [2019-10-02 01:03:59] /usr/bin/sort /app/public/converted_csv/antigua_barbuda__occurrences_14876.csv > /app/public/converted_csv/antigua_barbuda__occurrences_14876.csv_sorted
[CMD] [2019-10-02 01:04:00] /usr/bin/sort /app/public/converted_csv/antigua_barbuda__measurements_14877.csv > /app/public/converted_csv/antigua_barbuda__measurements_14877.csv_sorted
[STOP] [2019-10-02 01:04:02] convert_to_csv
[START] [2019-10-02 01:04:02] calculate_delta
[CMD] [2019-10-02 01:04:02] echo "0a" > /app/public/diff/antigua_barbuda__refs_14874.diff
[CMD] [2019-10-02 01:04:04] tail -n +1 /app/public/converted_csv/antigua_barbuda__refs_14874.csv >> /app/public/diff/antigua_barbuda__refs_14874.diff
[CMD] [2019-10-02 01:04:05] echo "." >> /app/public/diff/antigua_barbuda__refs_14874.diff
[CMD] [2019-10-02 01:04:07] echo "0a" > /app/public/diff/antigua_barbuda__nodes_14875.diff
[CMD] [2019-10-02 01:04:08] tail -n +1 /app/public/converted_csv/antigua_barbuda__nodes_14875.csv >> /app/public/diff/antigua_barbuda__nodes_14875.diff
[CMD] [2019-10-02 01:04:10] echo "." >> /app/public/diff/antigua_barbuda__nodes_14875.diff
[CMD] [2019-10-02 01:04:11] echo "0a" > /app/public/diff/antigua_barbuda__occurrences_14876.diff
[CMD] [2019-10-02 01:04:13] tail -n +1 /app/public/converted_csv/antigua_barbuda__occurrences_14876.csv >> /app/public/diff/antigua_barbuda__occurrences_14876.diff
[CMD] [2019-10-02 01:04:14] echo "." >> /app/public/diff/antigua_barbuda__occurrences_14876.diff
[CMD] [2019-10-02 01:04:16] echo "0a" > /app/public/diff/antigua_barbuda__measurements_14877.diff
[CMD] [2019-10-02 01:04:17] tail -n +1 /app/public/converted_csv/antigua_barbuda__measurements_14877.csv >> /app/public/diff/antigua_barbuda__measurements_14877.diff
[CMD] [2019-10-02 01:04:19] echo "." >> /app/public/diff/antigua_barbuda__measurements_14877.diff
[STOP] [2019-10-02 01:04:20] calculate_delta
[START] [2019-10-02 01:04:20] parse_diff_and_store
[INFO] [2019-10-02 01:04:22] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-02 01:04:23] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-02 01:04:25] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-02 01:04:27] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-02 01:04:30] Storing 2 References
[INFO] [2019-10-02 01:04:30] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-02 01:04:30] Average Time: 0.0
[INFO] [2019-10-02 01:04:30] Total Time: 1s
[INFO] [2019-10-02 01:04:30] Storing 1104 ScientificNames
[INFO] [2019-10-02 01:04:30] Processing group of 1104 in 2 groups of 1000
[INFO] [2019-10-02 01:04:30] Average Time: 0.25
[INFO] [2019-10-02 01:04:30] Total Time: 1s
[INFO] [2019-10-02 01:04:30] Storing 1104 Nodes
[INFO] [2019-10-02 01:04:30] Processing group of 1104 in 2 groups of 1000
[INFO] [2019-10-02 01:04:30] Average Time: 0.18
[INFO] [2019-10-02 01:04:30] Total Time: 1s
[INFO] [2019-10-02 01:04:30] Storing 482 Occurrences
[INFO] [2019-10-02 01:04:30] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-02 01:04:31] Average Time: 0.07
[INFO] [2019-10-02 01:04:31] Total Time: 1s
[INFO] [2019-10-02 01:04:31] Storing 1072 TraitsReferences
[INFO] [2019-10-02 01:04:31] Processing group of 1072 in 2 groups of 1000
[INFO] [2019-10-02 01:04:31] Average Time: 0.08
[INFO] [2019-10-02 01:04:31] Total Time: 1s
[INFO] [2019-10-02 01:04:31] Storing 1071 Traits
[INFO] [2019-10-02 01:04:31] Processing group of 1071 in 2 groups of 1000
[INFO] [2019-10-02 01:04:31] Average Time: 0.23
[INFO] [2019-10-02 01:04:31] Total Time: 1s
[INFO] [2019-10-02 01:04:31] Storing 1070 MetaTraits
[INFO] [2019-10-02 01:04:31] Processing group of 1070 in 2 groups of 1000
[INFO] [2019-10-02 01:04:31] Average Time: 0.09
[INFO] [2019-10-02 01:04:31] Total Time: 1s
[STOP] [2019-10-02 01:04:31] parse_diff_and_store
[START] [2019-10-02 01:04:31] resolve_keys
[INFO] [2019-10-02 01:04:39] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-02 01:04:39] traits to occurrences...
[INFO] [2019-10-02 01:04:40] traits to nodes (through occurrences)...
[INFO] [2019-10-02 01:04:40] Traits to sex term...
[INFO] [2019-10-02 01:04:40] Traits to lifestage term...
[INFO] [2019-10-02 01:04:41] MetaTraits to traits...
[INFO] [2019-10-02 01:04:41] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-02 01:04:41] Assocs to occurrences...
[INFO] [2019-10-02 01:04:41] Assocs to nodes...
[INFO] [2019-10-02 01:04:41] Assoc to sex term...
[INFO] [2019-10-02 01:04:41] Assoc to lifestage term...
[STOP] [2019-10-02 01:04:41] resolve_keys
[START] [2019-10-02 01:04:41] hold_for_later_1
[STOP] [2019-10-02 01:04:41] hold_for_later_1
[START] [2019-10-02 01:04:41] hold_for_later_2
[STOP] [2019-10-02 01:04:41] hold_for_later_2
[START] [2019-10-02 01:04:41] resolve_missing_parents
[STOP] [2019-10-02 01:04:42] resolve_missing_parents
[START] [2019-10-02 01:04:42] rebuild_nodes
[START] [2019-10-02 01:04:42] Flattener#flatten
[START] [2019-10-02 01:04:42] Flattener#study_resource
[START] [2019-10-02 01:04:42] Flattener#build_ancestry
[STOP] [2019-10-02 01:04:42] Flattener#build_ancestry
[INFO] [2019-10-02 01:04:42] 1104 ancestry keys
[START] [2019-10-02 01:04:42] build_node_ancestors
[INFO] [2019-10-02 01:04:42] old ancestors deleted.
[STOP] [2019-10-02 01:04:42] build_node_ancestors
[START] [2019-10-02 01:04:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 01:04:42] Flattener#propagate_ancestor_ids
[STOP] [2019-10-02 01:04:42] Flattener#flatten
[STOP] [2019-10-02 01:04:42] rebuild_nodes
[START] [2019-10-02 01:04:42] resolve_missing_media_owners
[STOP] [2019-10-02 01:04:42] resolve_missing_media_owners
[START] [2019-10-02 01:04:42] sanitize_media_verbatims
[STOP] [2019-10-02 01:04:42] sanitize_media_verbatims
[START] [2019-10-02 01:04:42] queue_downloads
[STOP] [2019-10-02 01:04:42] queue_downloads
[START] [2019-10-02 01:04:42] parse_names
[WARN] [2019-10-02 01:04:42] I see 1104 names which still need to be parsed.
[STOP] [2019-10-02 01:04:44] parse_names
[START] [2019-10-02 01:04:44] denormalize_canonical_names_to_nodes
[STOP] [2019-10-02 01:04:44] denormalize_canonical_names_to_nodes
[START] [2019-10-02 01:04:44] match_nodes
[START] [2019-10-02 01:04:44] map_all_nodes_to_pages
[STOP] [2019-10-02 01:05:33] map_all_nodes_to_pages
[INFO] [2019-10-02 01:05:33] 65 Unmatched nodes (of 1104)! That's too many to output. First 10: Coerebidae (#47668644); Thalaseus (#47668742); Thalaseus maximus (#47668741); Thalaseus sandvicensis (#47668847); Anas discors (#47668759); Anas clypeata (#47668915); Dendroica (#47669186); Dendroica petechia (#47669185); Technomyrmex difficilis (#47669138); Strumigenys emmae (#47669203)
[START] [2019-10-02 01:05:33] update_nodes
[STOP] [2019-10-02 01:05:34] update_nodes
[STOP] [2019-10-02 01:05:34] match_nodes
[START] [2019-10-02 01:05:34] reindex_search
[STOP] [2019-10-02 01:05:36] reindex_search
[START] [2019-10-02 01:05:36] normalize_units
[STOP] [2019-10-02 01:05:36] normalize_units
[START] [2019-10-02 01:05:36] calculate_statistics
[STOP] [2019-10-02 01:05:36] calculate_statistics
[START] [2019-10-02 01:05:36] complete_harvest_instance
[START] [2019-10-02 01:05:36] overall_tsv_creation
[INFO] [2019-10-02 01:05:36] Processing group of 1104 in 1 batches of 10000
[INFO] [2019-10-02 01:06:24] 482 Traits (unfiltered)...
[INFO] [2019-10-02 01:06:36] 482 Traits (filtered)...
[INFO] [2019-10-02 01:06:36] 0 Associations (filtered)...
[INFO] [2019-10-02 01:07:12] 2409 metadata added.
[INFO] [2019-10-02 01:07:12] 0 metadata added.
[INFO] [2019-10-02 01:07:12] Average Time: 74.72
[INFO] [2019-10-02 01:07:12] Total Time: 1m37s
[STOP] [2019-10-02 01:07:12] overall_tsv_creation
[INFO] [2019-10-02 01:07:12] Done. Check your files:
[INFO] [2019-10-02 01:07:14] (1104 lines) /app/public/data/antigua_barbuda_/publish_nodes.tsv
[INFO] [2019-10-02 01:07:15] (1297 lines) /app/public/data/antigua_barbuda_/publish_node_ancestors.tsv
[INFO] [2019-10-02 01:07:17] (1104 lines) /app/public/data/antigua_barbuda_/publish_scientific_names.tsv
[INFO] [2019-10-02 01:07:18] (483 lines) /app/public/data/antigua_barbuda_/publish_traits.tsv
[INFO] [2019-10-02 01:07:20] (2410 lines) /app/public/data/antigua_barbuda_/publish_metadata.tsv
[STOP] [2019-10-02 01:07:20] complete_harvest_instance
[START] [2019-10-02 01:07:20] completed
[STOP] [2019-10-02 01:07:20] completed
[STOP] [2019-10-02 01:07:20] logged process, took 204.82

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