Harvest for TaiEOL and NCHU Museum of Entomology Created 31 Dec 10:11

Stage: completed
Fetched: 31 Dec 10:11
Validated: 31 Dec 10:11
Deltas Created 31 Dec 10:11
Units Normalized: 31 Dec 10:12
Ancestry Built: 31 Dec 10:11
Nodes Matched: 31 Dec 10:12
Names Parsed: 31 Dec 10:11
New Models Stored: 31 Dec 10:11
Indexed: 31 Dec 10:12
Completed: 31 Dec 10:12
Time to Harvest: less than a minute
Harvesting Log

(133 lines)
# Logfile created on 2019-12-31 10:11:29 -0500 by logger.rb/56815
[START] [2019-12-31 10:11:29] logged process
[START] [2019-12-31 10:11:29] create_harvest_instance
[STOP] [2019-12-31 10:11:29] create_harvest_instance
[START] [2019-12-31 10:11:29] fetch_files
[STOP] [2019-12-31 10:11:29] fetch_files
[START] [2019-12-31 10:11:30] validate_each_file
[STOP] [2019-12-31 10:11:30] validate_each_file
[START] [2019-12-31 10:11:30] convert_to_csv
[CMD] [2019-12-31 10:11:30] /usr/bin/sort /app/public/converted_csv/tttme_agents_19833.csv > /app/public/converted_csv/tttme_agents_19833.csv_sorted
[CMD] [2019-12-31 10:11:30] /usr/bin/sort /app/public/converted_csv/tttme_nodes_19834.csv > /app/public/converted_csv/tttme_nodes_19834.csv_sorted
[CMD] [2019-12-31 10:11:30] /usr/bin/sort /app/public/converted_csv/tttme_media_19835.csv > /app/public/converted_csv/tttme_media_19835.csv_sorted
[CMD] [2019-12-31 10:11:30] /usr/bin/sort /app/public/converted_csv/tttme_vernaculars_19836.csv > /app/public/converted_csv/tttme_vernaculars_19836.csv_sorted
[STOP] [2019-12-31 10:11:30] convert_to_csv
[START] [2019-12-31 10:11:30] calculate_delta
[CMD] [2019-12-31 10:11:31] echo "0a" > /app/public/diff/tttme_agents_19833.diff
[CMD] [2019-12-31 10:11:31] tail -n +1 /app/public/converted_csv/tttme_agents_19833.csv >> /app/public/diff/tttme_agents_19833.diff
[CMD] [2019-12-31 10:11:31] echo "." >> /app/public/diff/tttme_agents_19833.diff
[CMD] [2019-12-31 10:11:31] echo "0a" > /app/public/diff/tttme_nodes_19834.diff
[CMD] [2019-12-31 10:11:31] tail -n +1 /app/public/converted_csv/tttme_nodes_19834.csv >> /app/public/diff/tttme_nodes_19834.diff
[CMD] [2019-12-31 10:11:31] echo "." >> /app/public/diff/tttme_nodes_19834.diff
[CMD] [2019-12-31 10:11:32] echo "0a" > /app/public/diff/tttme_media_19835.diff
[CMD] [2019-12-31 10:11:32] tail -n +1 /app/public/converted_csv/tttme_media_19835.csv >> /app/public/diff/tttme_media_19835.diff
[CMD] [2019-12-31 10:11:32] echo "." >> /app/public/diff/tttme_media_19835.diff
[CMD] [2019-12-31 10:11:32] echo "0a" > /app/public/diff/tttme_vernaculars_19836.diff
[CMD] [2019-12-31 10:11:32] tail -n +1 /app/public/converted_csv/tttme_vernaculars_19836.csv >> /app/public/diff/tttme_vernaculars_19836.diff
[CMD] [2019-12-31 10:11:32] echo "." >> /app/public/diff/tttme_vernaculars_19836.diff
[STOP] [2019-12-31 10:11:33] calculate_delta
[START] [2019-12-31 10:11:33] parse_diff_and_store
[INFO] [2019-12-31 10:11:33] Loading agents diff file into memory (true lines)...
[INFO] [2019-12-31 10:11:33] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-31 10:11:33] Loading media diff file into memory (true lines)...
[INFO] [2019-12-31 10:11:36] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-12-31 10:11:36] Storing 2 Attributions
[INFO] [2019-12-31 10:11:36] Processing group of 2 in 1 groups of 1000
[INFO] [2019-12-31 10:11:36] Average Time: 0.0
[INFO] [2019-12-31 10:11:36] Total Time: 1s
[INFO] [2019-12-31 10:11:36] Storing 165 ScientificNames
[INFO] [2019-12-31 10:11:36] Processing group of 165 in 1 groups of 1000
[INFO] [2019-12-31 10:11:36] Average Time: 0.18
[INFO] [2019-12-31 10:11:36] Total Time: 1s
[INFO] [2019-12-31 10:11:36] Storing 165 Nodes
[INFO] [2019-12-31 10:11:36] Processing group of 165 in 1 groups of 1000
[INFO] [2019-12-31 10:11:36] Average Time: 0.11
[INFO] [2019-12-31 10:11:36] Total Time: 1s
[INFO] [2019-12-31 10:11:36] Storing 2788 ContentAttributions
[INFO] [2019-12-31 10:11:36] Processing group of 2788 in 3 groups of 1000
[INFO] [2019-12-31 10:11:37] Average Time: 0.167
[INFO] [2019-12-31 10:11:37] Total Time: 1s
[INFO] [2019-12-31 10:11:37] Storing 1394 Media
[INFO] [2019-12-31 10:11:37] Processing group of 1394 in 2 groups of 1000
[INFO] [2019-12-31 10:11:37] Average Time: 0.395
[INFO] [2019-12-31 10:11:37] Total Time: 1s
[INFO] [2019-12-31 10:11:37] Storing 49 Vernaculars
[INFO] [2019-12-31 10:11:37] Processing group of 49 in 1 groups of 1000
[INFO] [2019-12-31 10:11:37] Average Time: 0.02
[INFO] [2019-12-31 10:11:37] Total Time: 1s
[STOP] [2019-12-31 10:11:37] parse_diff_and_store
[START] [2019-12-31 10:11:37] resolve_keys
[INFO] [2019-12-31 10:11:42] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-31 10:11:42] traits to occurrences...
[INFO] [2019-12-31 10:11:42] traits to nodes (through occurrences)...
[INFO] [2019-12-31 10:11:42] Traits to sex term...
[INFO] [2019-12-31 10:11:42] Traits to lifestage term...
[INFO] [2019-12-31 10:11:42] MetaTraits to traits...
[INFO] [2019-12-31 10:11:42] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-31 10:11:42] Assocs to occurrences...
[INFO] [2019-12-31 10:11:42] Assocs to nodes...
[INFO] [2019-12-31 10:11:42] Assoc to sex term...
[INFO] [2019-12-31 10:11:42] Assoc to lifestage term...
[STOP] [2019-12-31 10:11:42] resolve_keys
[START] [2019-12-31 10:11:42] hold_for_later_1
[STOP] [2019-12-31 10:11:42] hold_for_later_1
[START] [2019-12-31 10:11:42] hold_for_later_2
[STOP] [2019-12-31 10:11:42] hold_for_later_2
[START] [2019-12-31 10:11:42] resolve_missing_parents
[STOP] [2019-12-31 10:11:42] resolve_missing_parents
[START] [2019-12-31 10:11:42] rebuild_nodes
[START] [2019-12-31 10:11:42] Flattener#flatten
[START] [2019-12-31 10:11:42] Flattener#study_resource
[START] [2019-12-31 10:11:42] Flattener#build_ancestry
[STOP] [2019-12-31 10:11:42] Flattener#build_ancestry
[INFO] [2019-12-31 10:11:42] 165 ancestry keys
[START] [2019-12-31 10:11:42] build_node_ancestors
[INFO] [2019-12-31 10:11:42] old ancestors deleted.
[STOP] [2019-12-31 10:11:42] build_node_ancestors
[START] [2019-12-31 10:11:42] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:11:42] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:11:42] Flattener#flatten
[STOP] [2019-12-31 10:11:42] rebuild_nodes
[START] [2019-12-31 10:11:42] resolve_missing_media_owners
[STOP] [2019-12-31 10:11:42] resolve_missing_media_owners
[START] [2019-12-31 10:11:42] sanitize_media_verbatims
[STOP] [2019-12-31 10:11:42] sanitize_media_verbatims
[START] [2019-12-31 10:11:42] queue_downloads
[STOP] [2019-12-31 10:11:42] queue_downloads
[START] [2019-12-31 10:11:42] parse_names
[WARN] [2019-12-31 10:11:42] I see 165 names which still need to be parsed.
[STOP] [2019-12-31 10:11:44] parse_names
[START] [2019-12-31 10:11:44] denormalize_canonical_names_to_nodes
[STOP] [2019-12-31 10:11:44] denormalize_canonical_names_to_nodes
[START] [2019-12-31 10:11:44] match_nodes
[START] [2019-12-31 10:11:44] map_all_nodes_to_pages
[STOP] [2019-12-31 10:12:08] map_all_nodes_to_pages
[INFO] [2019-12-31 10:12:08] ZERO unmatched nodes (of 165)! Nicely done.
[START] [2019-12-31 10:12:08] update_nodes
[STOP] [2019-12-31 10:12:08] update_nodes
[STOP] [2019-12-31 10:12:08] match_nodes
[START] [2019-12-31 10:12:08] reindex_search
[STOP] [2019-12-31 10:12:08] reindex_search
[START] [2019-12-31 10:12:08] normalize_units
[STOP] [2019-12-31 10:12:08] normalize_units
[START] [2019-12-31 10:12:08] calculate_statistics
[STOP] [2019-12-31 10:12:08] calculate_statistics
[START] [2019-12-31 10:12:08] complete_harvest_instance
[START] [2019-12-31 10:12:08] overall_tsv_creation
[INFO] [2019-12-31 10:12:08] Processing group of 165 in 1 batches of 10000
[INFO] [2019-12-31 10:12:46] Average Time: 14.35
[INFO] [2019-12-31 10:12:46] Total Time: 39s
[STOP] [2019-12-31 10:12:46] overall_tsv_creation
[INFO] [2019-12-31 10:12:46] Done. Check your files:
[INFO] [2019-12-31 10:12:47] (165 lines) /app/public/data/tttme/publish_nodes.tsv
[INFO] [2019-12-31 10:12:47] (475 lines) /app/public/data/tttme/publish_node_ancestors.tsv
[INFO] [2019-12-31 10:12:47] (165 lines) /app/public/data/tttme/publish_scientific_names.tsv
[INFO] [2019-12-31 10:12:47] (1394 lines) /app/public/data/tttme/publish_media.tsv
[INFO] [2019-12-31 10:12:47] (104 lines) /app/public/data/tttme/publish_image_info.tsv
[INFO] [2019-12-31 10:12:47] (49 lines) /app/public/data/tttme/publish_vernaculars.tsv
[INFO] [2019-12-31 10:12:48] (2788 lines) /app/public/data/tttme/publish_attributions.tsv
[STOP] [2019-12-31 10:12:48] complete_harvest_instance
[START] [2019-12-31 10:12:48] completed
[STOP] [2019-12-31 10:12:48] completed
[STOP] [2019-12-31 10:12:48] logged process, took 79.08
[ERR] [2019-12-31 10:18:11][hdls] download_and_prep FAILED for Medium.find(10379187): 403 Forbidden
Latest Process

31 Dec 10:11 EXITED currently processing 0