Harvest for SERPENT Project Created 11 Oct 17:15

Stage: completed
Fetched: 11 Oct 17:15
Validated: 11 Oct 17:15
Deltas Created 11 Oct 17:16
Units Normalized: 11 Oct 17:16
Ancestry Built: 11 Oct 17:16
Nodes Matched: 11 Oct 17:16
Names Parsed: 11 Oct 17:16
New Models Stored: 11 Oct 17:16
Indexed: 11 Oct 17:16
Completed: 11 Oct 17:17
Time to Harvest: less than a minute
Harvesting Log

(141 lines)
# Logfile created on 2019-10-11 17:15:59 -0400 by logger.rb/56815
[START] [2019-10-11 17:15:59] logged process
[START] [2019-10-11 17:15:59] create_harvest_instance
[STOP] [2019-10-11 17:15:59] create_harvest_instance
[START] [2019-10-11 17:15:59] fetch_files
[STOP] [2019-10-11 17:15:59] fetch_files
[START] [2019-10-11 17:15:59] validate_each_file
[STOP] [2019-10-11 17:15:59] validate_each_file
[START] [2019-10-11 17:15:59] convert_to_csv
[CMD] [2019-10-11 17:15:59] /usr/bin/sort /app/public/converted_csv/serpent_project__nodes_15279.csv > /app/public/converted_csv/serpent_project__nodes_15279.csv_sorted
[CMD] [2019-10-11 17:15:59] /usr/bin/sort /app/public/converted_csv/serpent_project__media_15280.csv > /app/public/converted_csv/serpent_project__media_15280.csv_sorted
[STOP] [2019-10-11 17:16:00] convert_to_csv
[START] [2019-10-11 17:16:00] calculate_delta
[CMD] [2019-10-11 17:16:00] echo "0a" > /app/public/diff/serpent_project__nodes_15279.diff
[CMD] [2019-10-11 17:16:00] tail -n +1 /app/public/converted_csv/serpent_project__nodes_15279.csv >> /app/public/diff/serpent_project__nodes_15279.diff
[CMD] [2019-10-11 17:16:00] echo "." >> /app/public/diff/serpent_project__nodes_15279.diff
[CMD] [2019-10-11 17:16:00] echo "0a" > /app/public/diff/serpent_project__media_15280.diff
[CMD] [2019-10-11 17:16:00] tail -n +1 /app/public/converted_csv/serpent_project__media_15280.csv >> /app/public/diff/serpent_project__media_15280.diff
[CMD] [2019-10-11 17:16:00] echo "." >> /app/public/diff/serpent_project__media_15280.diff
[STOP] [2019-10-11 17:16:00] calculate_delta
[START] [2019-10-11 17:16:00] parse_diff_and_store
[INFO] [2019-10-11 17:16:00] Loading nodes diff file into memory (true lines)...
[WARN] [2019-10-11 17:16:00] Filtered Scientific Name `Hyalonema\tapertum` to `Hyalonematapertum`
[WARN] [2019-10-11 17:16:00] Filtered Scientific Name `Madrepora\toculata` to `Madreporatoculata`
[INFO] [2019-10-11 17:16:00] Loading media diff file into memory (true lines)...
[INFO] [2019-10-11 17:16:03] Storing 624 ScientificNames
[INFO] [2019-10-11 17:16:03] Processing group of 624 in 1 groups of 1000
[INFO] [2019-10-11 17:16:04] Average Time: 0.35
[INFO] [2019-10-11 17:16:04] Total Time: 1s
[INFO] [2019-10-11 17:16:04] Storing 624 Nodes
[INFO] [2019-10-11 17:16:04] Processing group of 624 in 1 groups of 1000
[INFO] [2019-10-11 17:16:04] Average Time: 0.24
[INFO] [2019-10-11 17:16:04] Total Time: 1s
[INFO] [2019-10-11 17:16:04] Storing 1859 Media
[INFO] [2019-10-11 17:16:04] Processing group of 1859 in 2 groups of 1000
[INFO] [2019-10-11 17:16:05] Average Time: 0.45
[INFO] [2019-10-11 17:16:05] Total Time: 1s
[STOP] [2019-10-11 17:16:05] parse_diff_and_store
[START] [2019-10-11 17:16:05] resolve_keys
[INFO] [2019-10-11 17:16:09] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 17:16:09] traits to occurrences...
[INFO] [2019-10-11 17:16:09] traits to nodes (through occurrences)...
[INFO] [2019-10-11 17:16:09] Traits to sex term...
[INFO] [2019-10-11 17:16:09] Traits to lifestage term...
[INFO] [2019-10-11 17:16:09] MetaTraits to traits...
[INFO] [2019-10-11 17:16:09] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 17:16:09] Assocs to occurrences...
[INFO] [2019-10-11 17:16:09] Assocs to nodes...
[INFO] [2019-10-11 17:16:09] Assoc to sex term...
[INFO] [2019-10-11 17:16:09] Assoc to lifestage term...
[STOP] [2019-10-11 17:16:09] resolve_keys
[START] [2019-10-11 17:16:09] hold_for_later_1
[STOP] [2019-10-11 17:16:09] hold_for_later_1
[START] [2019-10-11 17:16:09] hold_for_later_2
[STOP] [2019-10-11 17:16:09] hold_for_later_2
[START] [2019-10-11 17:16:09] resolve_missing_parents
[STOP] [2019-10-11 17:16:09] resolve_missing_parents
[START] [2019-10-11 17:16:09] rebuild_nodes
[START] [2019-10-11 17:16:09] Flattener#flatten
[START] [2019-10-11 17:16:09] Flattener#study_resource
[START] [2019-10-11 17:16:09] Flattener#build_ancestry
[STOP] [2019-10-11 17:16:09] Flattener#build_ancestry
[INFO] [2019-10-11 17:16:09] 624 ancestry keys
[START] [2019-10-11 17:16:09] build_node_ancestors
[INFO] [2019-10-11 17:16:09] old ancestors deleted.
[STOP] [2019-10-11 17:16:09] build_node_ancestors
[START] [2019-10-11 17:16:09] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 17:16:09] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 17:16:09] Flattener#flatten
[STOP] [2019-10-11 17:16:09] rebuild_nodes
[START] [2019-10-11 17:16:09] resolve_missing_media_owners
[STOP] [2019-10-11 17:16:09] resolve_missing_media_owners
[START] [2019-10-11 17:16:09] sanitize_media_verbatims
[STOP] [2019-10-11 17:16:09] sanitize_media_verbatims
[START] [2019-10-11 17:16:09] queue_downloads
[STOP] [2019-10-11 17:16:09] queue_downloads
[START] [2019-10-11 17:16:09] parse_names
[WARN] [2019-10-11 17:16:09] I see 624 names which still need to be parsed.
[WARN] [2019-10-11 17:16:11] I see 5 names which still need to be parsed.
[STOP] [2019-10-11 17:16:12] parse_names
[START] [2019-10-11 17:16:12] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 17:16:12] denormalize_canonical_names_to_nodes
[START] [2019-10-11 17:16:12] match_nodes
[START] [2019-10-11 17:16:12] map_all_nodes_to_pages
[ERR] [2019-10-11 17:16:16][hdls] download_and_prep FAILED for Medium.find(10256317): 404 Not Found
[ERR] [2019-10-11 17:16:17][hdls] download_and_prep FAILED for Medium.find(10256333): 404 Not Found
[ERR] [2019-10-11 17:16:17][hdls] download_and_prep FAILED for Medium.find(10256334): 404 Not Found
[ERR] [2019-10-11 17:16:18][hdls] download_and_prep FAILED for Medium.find(10256336): 404 Not Found
[ERR] [2019-10-11 17:16:18][hdls] download_and_prep FAILED for Medium.find(10256335): 404 Not Found
[ERR] [2019-10-11 17:16:18][hdls] download_and_prep FAILED for Medium.find(10256337): 404 Not Found
[ERR] [2019-10-11 17:16:36][hdls] download_and_prep FAILED for Medium.find(10256625): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256969): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256968): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256970): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256972): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256971): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256968): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256973): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256974): 404 Not Found
[ERR] [2019-10-11 17:16:55][hdls] download_and_prep FAILED for Medium.find(10256975): 404 Not Found
[STOP] [2019-10-11 17:16:55] map_all_nodes_to_pages
[INFO] [2019-10-11 17:16:55] 64 Unmatched nodes (of 624)! That's too many to output. First 10: Caryoplyllia (#48861379); Madreporatoculata (#48861610); Pennatulid (#48861727); Pomatocerus (#48861753); Sardo (#48861801); Chimaera or genus (#48861402); Cittopsis rosea (#48861420); Corphaenoides (#48861435); Coryphaenoides amatus (#48861439); Glyptocephalus cynologus (#48861518)
[START] [2019-10-11 17:16:55] update_nodes
[STOP] [2019-10-11 17:16:56] update_nodes
[STOP] [2019-10-11 17:16:56] match_nodes
[START] [2019-10-11 17:16:56] reindex_search
[STOP] [2019-10-11 17:16:57] reindex_search
[START] [2019-10-11 17:16:57] normalize_units
[STOP] [2019-10-11 17:16:57] normalize_units
[START] [2019-10-11 17:16:57] calculate_statistics
[STOP] [2019-10-11 17:16:57] calculate_statistics
[START] [2019-10-11 17:16:57] complete_harvest_instance
[START] [2019-10-11 17:16:57] overall_tsv_creation
[INFO] [2019-10-11 17:16:57] Processing group of 624 in 1 batches of 10000
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257213): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257214): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257215): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257216): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257217): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257218): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257219): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257220): 404 Not Found
[ERR] [2019-10-11 17:17:07][hdls] download_and_prep FAILED for Medium.find(10257217): 404 Not Found
[ERR] [2019-10-11 17:17:14][hdls] download_and_prep FAILED for Medium.find(10257341): 404 Not Found
[ERR] [2019-10-11 17:17:14][hdls] download_and_prep FAILED for Medium.find(10257346): 404 Not Found
[ERR] [2019-10-11 17:17:17][hdls] download_and_prep FAILED for Medium.find(10257389): 404 Not Found
[ERR] [2019-10-11 17:17:17][hdls] download_and_prep FAILED for Medium.find(10257401): 404 Not Found
[ERR] [2019-10-11 17:17:19][hdls] download_and_prep FAILED for Medium.find(10257441): 404 Not Found
[INFO] [2019-10-11 17:17:39] Average Time: 19.27
[INFO] [2019-10-11 17:17:39] Total Time: 43s
[STOP] [2019-10-11 17:17:39] overall_tsv_creation
[INFO] [2019-10-11 17:17:39] Done. Check your files:
[INFO] [2019-10-11 17:17:39] (623 lines) /app/public/data/serpent_project_/publish_nodes.tsv
[INFO] [2019-10-11 17:17:40] (1831 lines) /app/public/data/serpent_project_/publish_node_ancestors.tsv
[INFO] [2019-10-11 17:17:40] (624 lines) /app/public/data/serpent_project_/publish_scientific_names.tsv
[INFO] [2019-10-11 17:17:40] (1859 lines) /app/public/data/serpent_project_/publish_media.tsv
[INFO] [2019-10-11 17:17:40] (753 lines) /app/public/data/serpent_project_/publish_image_info.tsv
[STOP] [2019-10-11 17:17:40] complete_harvest_instance
[START] [2019-10-11 17:17:40] completed
[STOP] [2019-10-11 17:17:40] completed
[STOP] [2019-10-11 17:17:40] logged process, took 101.17
Latest Process

11 Oct 17:15 EXITED currently processing 0