Harvest for Japan Agency for Marine-Earth Science and Technology Created 11 Oct 15:35

Stage: completed
Fetched: 11 Oct 15:35
Validated: 11 Oct 15:35
Deltas Created 11 Oct 15:35
Units Normalized: 11 Oct 15:37
Ancestry Built: 11 Oct 15:36
Nodes Matched: 11 Oct 15:37
Names Parsed: 11 Oct 15:36
New Models Stored: 11 Oct 15:35
Indexed: 11 Oct 15:37
Completed: 11 Oct 15:38
Time to Harvest: less than a minute

Harvesting Log

(114 lines)
# Logfile created on 2019-10-11 15:35:56 -0400 by logger.rb/56815
[START] [2019-10-11 15:35:56] logged process
[START] [2019-10-11 15:35:56] create_harvest_instance
[STOP] [2019-10-11 15:35:57] create_harvest_instance
[START] [2019-10-11 15:35:57] fetch_files
[STOP] [2019-10-11 15:35:57] fetch_files
[START] [2019-10-11 15:35:57] validate_each_file
[STOP] [2019-10-11 15:35:57] validate_each_file
[START] [2019-10-11 15:35:57] convert_to_csv
[CMD] [2019-10-11 15:35:57] /usr/bin/sort /app/public/converted_csv/jamstec_dw_jamst_nodes_15182.csv > /app/public/converted_csv/jamstec_dw_jamst_nodes_15182.csv_sorted
[CMD] [2019-10-11 15:35:57] /usr/bin/sort /app/public/converted_csv/jamstec_dw_jamst_media_15183.csv > /app/public/converted_csv/jamstec_dw_jamst_media_15183.csv_sorted
[STOP] [2019-10-11 15:35:57] convert_to_csv
[START] [2019-10-11 15:35:57] calculate_delta
[CMD] [2019-10-11 15:35:57] echo "0a" > /app/public/diff/jamstec_dw_jamst_nodes_15182.diff
[CMD] [2019-10-11 15:35:57] tail -n +1 /app/public/converted_csv/jamstec_dw_jamst_nodes_15182.csv >> /app/public/diff/jamstec_dw_jamst_nodes_15182.diff
[CMD] [2019-10-11 15:35:57] echo "." >> /app/public/diff/jamstec_dw_jamst_nodes_15182.diff
[CMD] [2019-10-11 15:35:57] echo "0a" > /app/public/diff/jamstec_dw_jamst_media_15183.diff
[CMD] [2019-10-11 15:35:57] tail -n +1 /app/public/converted_csv/jamstec_dw_jamst_media_15183.csv >> /app/public/diff/jamstec_dw_jamst_media_15183.diff
[CMD] [2019-10-11 15:35:57] echo "." >> /app/public/diff/jamstec_dw_jamst_media_15183.diff
[STOP] [2019-10-11 15:35:57] calculate_delta
[START] [2019-10-11 15:35:57] parse_diff_and_store
[INFO] [2019-10-11 15:35:57] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-11 15:35:57] Loading media diff file into memory (true lines)...
[INFO] [2019-10-11 15:35:58] Storing 1230 ScientificNames
[INFO] [2019-10-11 15:35:58] Processing group of 1230 in 2 groups of 1000
[INFO] [2019-10-11 15:35:58] Average Time: 0.295
[INFO] [2019-10-11 15:35:58] Total Time: 1s
[INFO] [2019-10-11 15:35:58] Storing 1230 Nodes
[INFO] [2019-10-11 15:35:58] Processing group of 1230 in 2 groups of 1000
[INFO] [2019-10-11 15:35:59] Average Time: 0.265
[INFO] [2019-10-11 15:35:59] Total Time: 1s
[INFO] [2019-10-11 15:35:59] Storing 498 BibliographicCitations
[INFO] [2019-10-11 15:35:59] Processing group of 498 in 1 groups of 1000
[INFO] [2019-10-11 15:35:59] Average Time: 0.1
[INFO] [2019-10-11 15:35:59] Total Time: 1s
[INFO] [2019-10-11 15:35:59] Storing 498 Media
[INFO] [2019-10-11 15:35:59] Processing group of 498 in 1 groups of 1000
[INFO] [2019-10-11 15:35:59] Average Time: 0.32
[INFO] [2019-10-11 15:35:59] Total Time: 1s
[STOP] [2019-10-11 15:35:59] parse_diff_and_store
[START] [2019-10-11 15:35:59] resolve_keys
[INFO] [2019-10-11 15:36:05] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-11 15:36:05] traits to occurrences...
[INFO] [2019-10-11 15:36:05] traits to nodes (through occurrences)...
[INFO] [2019-10-11 15:36:05] Traits to sex term...
[INFO] [2019-10-11 15:36:05] Traits to lifestage term...
[INFO] [2019-10-11 15:36:05] MetaTraits to traits...
[INFO] [2019-10-11 15:36:05] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-11 15:36:05] Assocs to occurrences...
[INFO] [2019-10-11 15:36:05] Assocs to nodes...
[INFO] [2019-10-11 15:36:05] Assoc to sex term...
[INFO] [2019-10-11 15:36:05] Assoc to lifestage term...
[STOP] [2019-10-11 15:36:05] resolve_keys
[START] [2019-10-11 15:36:05] hold_for_later_1
[STOP] [2019-10-11 15:36:05] hold_for_later_1
[START] [2019-10-11 15:36:05] hold_for_later_2
[STOP] [2019-10-11 15:36:05] hold_for_later_2
[START] [2019-10-11 15:36:05] resolve_missing_parents
[STOP] [2019-10-11 15:36:05] resolve_missing_parents
[START] [2019-10-11 15:36:05] rebuild_nodes
[START] [2019-10-11 15:36:05] Flattener#flatten
[START] [2019-10-11 15:36:05] Flattener#study_resource
[START] [2019-10-11 15:36:05] Flattener#build_ancestry
[STOP] [2019-10-11 15:36:05] Flattener#build_ancestry
[INFO] [2019-10-11 15:36:05] 1230 ancestry keys
[START] [2019-10-11 15:36:05] build_node_ancestors
[INFO] [2019-10-11 15:36:05] old ancestors deleted.
[STOP] [2019-10-11 15:36:06] build_node_ancestors
[START] [2019-10-11 15:36:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 15:36:06] Flattener#propagate_ancestor_ids
[STOP] [2019-10-11 15:36:06] Flattener#flatten
[STOP] [2019-10-11 15:36:06] rebuild_nodes
[START] [2019-10-11 15:36:06] resolve_missing_media_owners
[STOP] [2019-10-11 15:36:06] resolve_missing_media_owners
[START] [2019-10-11 15:36:06] sanitize_media_verbatims
[STOP] [2019-10-11 15:36:06] sanitize_media_verbatims
[START] [2019-10-11 15:36:06] queue_downloads
[STOP] [2019-10-11 15:36:06] queue_downloads
[START] [2019-10-11 15:36:06] parse_names
[WARN] [2019-10-11 15:36:06] I see 1230 names which still need to be parsed.
[WARN] [2019-10-11 15:36:09] I see 82 names which still need to be parsed.
[STOP] [2019-10-11 15:36:10] parse_names
[START] [2019-10-11 15:36:10] denormalize_canonical_names_to_nodes
[STOP] [2019-10-11 15:36:10] denormalize_canonical_names_to_nodes
[START] [2019-10-11 15:36:10] match_nodes
[START] [2019-10-11 15:36:10] map_all_nodes_to_pages
[STOP] [2019-10-11 15:37:44] map_all_nodes_to_pages
[INFO] [2019-10-11 15:37:44] 124 Unmatched nodes (of 1230)! That's too many to output. First 10: Melanostomiinae (#48788798); Appendicularia (#48789310); Agnatha (#48789276); Pisciformes (#48789782); Bathygadinae (#48789344); Macrourinae (#48789626); Neobythitinae (#48789673); Synagropinae (#48789918); Scombroidei (#48789858); Trachinoidei (#48789945)
[START] [2019-10-11 15:37:44] update_nodes
[STOP] [2019-10-11 15:37:45] update_nodes
[STOP] [2019-10-11 15:37:45] match_nodes
[START] [2019-10-11 15:37:45] reindex_search
[STOP] [2019-10-11 15:37:46] reindex_search
[START] [2019-10-11 15:37:46] normalize_units
[STOP] [2019-10-11 15:37:46] normalize_units
[START] [2019-10-11 15:37:46] calculate_statistics
[STOP] [2019-10-11 15:37:46] calculate_statistics
[START] [2019-10-11 15:37:46] complete_harvest_instance
[START] [2019-10-11 15:37:46] overall_tsv_creation
[INFO] [2019-10-11 15:37:46] Processing group of 1230 in 1 batches of 10000
[INFO] [2019-10-11 15:38:25] Average Time: 17.72
[INFO] [2019-10-11 15:38:25] Total Time: 40s
[STOP] [2019-10-11 15:38:25] overall_tsv_creation
[INFO] [2019-10-11 15:38:25] Done. Check your files:
[INFO] [2019-10-11 15:38:25] (498 lines) /app/public/data/jamstec_dw_jamst/publish_bibliographic_citations.tsv
[INFO] [2019-10-11 15:38:25] (1230 lines) /app/public/data/jamstec_dw_jamst/publish_nodes.tsv
[INFO] [2019-10-11 15:38:25] (5744 lines) /app/public/data/jamstec_dw_jamst/publish_node_ancestors.tsv
[INFO] [2019-10-11 15:38:25] (1230 lines) /app/public/data/jamstec_dw_jamst/publish_scientific_names.tsv
[INFO] [2019-10-11 15:38:25] (498 lines) /app/public/data/jamstec_dw_jamst/publish_media.tsv
[INFO] [2019-10-11 15:38:25] (498 lines) /app/public/data/jamstec_dw_jamst/publish_image_info.tsv
[STOP] [2019-10-11 15:38:25] complete_harvest_instance
[START] [2019-10-11 15:38:25] completed
[STOP] [2019-10-11 15:38:25] completed
[STOP] [2019-10-11 15:38:25] logged process, took 149.59

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