Harvest for Monaco Species List Created 14 Oct 09:09

Stage: completed
Fetched: 14 Oct 09:09
Validated: 14 Oct 09:09
Deltas Created 14 Oct 09:09
Units Normalized: 14 Oct 09:10
Ancestry Built: 14 Oct 09:09
Nodes Matched: 14 Oct 09:10
Names Parsed: 14 Oct 09:09
New Models Stored: 14 Oct 09:09
Indexed: 14 Oct 09:10
Completed: 14 Oct 09:11
Time to Harvest: less than a minute

Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 09:09:42 -0400 by logger.rb/56815
[START] [2019-10-14 09:09:42] logged process
[START] [2019-10-14 09:09:42] create_harvest_instance
[STOP] [2019-10-14 09:09:42] create_harvest_instance
[START] [2019-10-14 09:09:42] fetch_files
[STOP] [2019-10-14 09:09:42] fetch_files
[START] [2019-10-14 09:09:42] validate_each_file
[STOP] [2019-10-14 09:09:42] validate_each_file
[START] [2019-10-14 09:09:42] convert_to_csv
[CMD] [2019-10-14 09:09:42] /usr/bin/sort /app/public/converted_csv/monaco_sp_list_refs_16603.csv > /app/public/converted_csv/monaco_sp_list_refs_16603.csv_sorted
[CMD] [2019-10-14 09:09:42] /usr/bin/sort /app/public/converted_csv/monaco_sp_list_nodes_16604.csv > /app/public/converted_csv/monaco_sp_list_nodes_16604.csv_sorted
[CMD] [2019-10-14 09:09:43] /usr/bin/sort /app/public/converted_csv/monaco_sp_list_occurrences_16605.csv > /app/public/converted_csv/monaco_sp_list_occurrences_16605.csv_sorted
[CMD] [2019-10-14 09:09:43] /usr/bin/sort /app/public/converted_csv/monaco_sp_list_measurements_16606.csv > /app/public/converted_csv/monaco_sp_list_measurements_16606.csv_sorted
[STOP] [2019-10-14 09:09:43] convert_to_csv
[START] [2019-10-14 09:09:43] calculate_delta
[CMD] [2019-10-14 09:09:43] echo "0a" > /app/public/diff/monaco_sp_list_refs_16603.diff
[CMD] [2019-10-14 09:09:43] tail -n +1 /app/public/converted_csv/monaco_sp_list_refs_16603.csv >> /app/public/diff/monaco_sp_list_refs_16603.diff
[CMD] [2019-10-14 09:09:43] echo "." >> /app/public/diff/monaco_sp_list_refs_16603.diff
[CMD] [2019-10-14 09:09:43] echo "0a" > /app/public/diff/monaco_sp_list_nodes_16604.diff
[CMD] [2019-10-14 09:09:43] tail -n +1 /app/public/converted_csv/monaco_sp_list_nodes_16604.csv >> /app/public/diff/monaco_sp_list_nodes_16604.diff
[CMD] [2019-10-14 09:09:43] echo "." >> /app/public/diff/monaco_sp_list_nodes_16604.diff
[CMD] [2019-10-14 09:09:43] echo "0a" > /app/public/diff/monaco_sp_list_occurrences_16605.diff
[CMD] [2019-10-14 09:09:43] tail -n +1 /app/public/converted_csv/monaco_sp_list_occurrences_16605.csv >> /app/public/diff/monaco_sp_list_occurrences_16605.diff
[CMD] [2019-10-14 09:09:43] echo "." >> /app/public/diff/monaco_sp_list_occurrences_16605.diff
[CMD] [2019-10-14 09:09:44] echo "0a" > /app/public/diff/monaco_sp_list_measurements_16606.diff
[CMD] [2019-10-14 09:09:44] tail -n +1 /app/public/converted_csv/monaco_sp_list_measurements_16606.csv >> /app/public/diff/monaco_sp_list_measurements_16606.diff
[CMD] [2019-10-14 09:09:44] echo "." >> /app/public/diff/monaco_sp_list_measurements_16606.diff
[STOP] [2019-10-14 09:09:44] calculate_delta
[START] [2019-10-14 09:09:44] parse_diff_and_store
[INFO] [2019-10-14 09:09:44] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 09:09:44] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 09:09:44] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 09:09:44] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 09:09:45] Storing 2 References
[INFO] [2019-10-14 09:09:45] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 09:09:45] Average Time: 0.0
[INFO] [2019-10-14 09:09:45] Total Time: 1s
[INFO] [2019-10-14 09:09:45] Storing 282 ScientificNames
[INFO] [2019-10-14 09:09:45] Processing group of 282 in 1 groups of 1000
[INFO] [2019-10-14 09:09:45] Average Time: 0.18
[INFO] [2019-10-14 09:09:45] Total Time: 1s
[INFO] [2019-10-14 09:09:45] Storing 282 Nodes
[INFO] [2019-10-14 09:09:45] Processing group of 282 in 1 groups of 1000
[INFO] [2019-10-14 09:09:45] Average Time: 0.08
[INFO] [2019-10-14 09:09:45] Total Time: 1s
[INFO] [2019-10-14 09:09:45] Storing 99 Occurrences
[INFO] [2019-10-14 09:09:45] Processing group of 99 in 1 groups of 1000
[INFO] [2019-10-14 09:09:45] Average Time: 0.02
[INFO] [2019-10-14 09:09:45] Total Time: 1s
[INFO] [2019-10-14 09:09:45] Storing 198 TraitsReferences
[INFO] [2019-10-14 09:09:45] Processing group of 198 in 1 groups of 1000
[INFO] [2019-10-14 09:09:45] Average Time: 0.1
[INFO] [2019-10-14 09:09:45] Total Time: 1s
[INFO] [2019-10-14 09:09:45] Storing 198 Traits
[INFO] [2019-10-14 09:09:45] Processing group of 198 in 1 groups of 1000
[INFO] [2019-10-14 09:09:46] Average Time: 0.18
[INFO] [2019-10-14 09:09:46] Total Time: 1s
[INFO] [2019-10-14 09:09:46] Storing 198 MetaTraits
[INFO] [2019-10-14 09:09:46] Processing group of 198 in 1 groups of 1000
[INFO] [2019-10-14 09:09:46] Average Time: 0.05
[INFO] [2019-10-14 09:09:46] Total Time: 1s
[STOP] [2019-10-14 09:09:46] parse_diff_and_store
[START] [2019-10-14 09:09:46] resolve_keys
[INFO] [2019-10-14 09:09:50] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 09:09:50] traits to occurrences...
[INFO] [2019-10-14 09:09:50] traits to nodes (through occurrences)...
[INFO] [2019-10-14 09:09:50] Traits to sex term...
[INFO] [2019-10-14 09:09:50] Traits to lifestage term...
[INFO] [2019-10-14 09:09:50] MetaTraits to traits...
[INFO] [2019-10-14 09:09:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 09:09:50] Assocs to occurrences...
[INFO] [2019-10-14 09:09:50] Assocs to nodes...
[INFO] [2019-10-14 09:09:50] Assoc to sex term...
[INFO] [2019-10-14 09:09:50] Assoc to lifestage term...
[STOP] [2019-10-14 09:09:50] resolve_keys
[START] [2019-10-14 09:09:50] hold_for_later_1
[STOP] [2019-10-14 09:09:50] hold_for_later_1
[START] [2019-10-14 09:09:50] hold_for_later_2
[STOP] [2019-10-14 09:09:50] hold_for_later_2
[START] [2019-10-14 09:09:50] resolve_missing_parents
[STOP] [2019-10-14 09:09:50] resolve_missing_parents
[START] [2019-10-14 09:09:50] rebuild_nodes
[START] [2019-10-14 09:09:50] Flattener#flatten
[START] [2019-10-14 09:09:50] Flattener#study_resource
[START] [2019-10-14 09:09:50] Flattener#build_ancestry
[STOP] [2019-10-14 09:09:50] Flattener#build_ancestry
[INFO] [2019-10-14 09:09:50] 282 ancestry keys
[START] [2019-10-14 09:09:50] build_node_ancestors
[INFO] [2019-10-14 09:09:50] old ancestors deleted.
[STOP] [2019-10-14 09:09:50] build_node_ancestors
[START] [2019-10-14 09:09:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:09:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 09:09:50] Flattener#flatten
[STOP] [2019-10-14 09:09:50] rebuild_nodes
[START] [2019-10-14 09:09:50] resolve_missing_media_owners
[STOP] [2019-10-14 09:09:50] resolve_missing_media_owners
[START] [2019-10-14 09:09:50] sanitize_media_verbatims
[STOP] [2019-10-14 09:09:50] sanitize_media_verbatims
[START] [2019-10-14 09:09:50] queue_downloads
[STOP] [2019-10-14 09:09:50] queue_downloads
[START] [2019-10-14 09:09:50] parse_names
[WARN] [2019-10-14 09:09:50] I see 282 names which still need to be parsed.
[STOP] [2019-10-14 09:09:52] parse_names
[START] [2019-10-14 09:09:52] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 09:09:52] denormalize_canonical_names_to_nodes
[START] [2019-10-14 09:09:52] match_nodes
[START] [2019-10-14 09:09:52] map_all_nodes_to_pages
[STOP] [2019-10-14 09:10:20] map_all_nodes_to_pages
[INFO] [2019-10-14 09:10:20] Unmatched nodes (10 of 282): Thalaseus (#50783284); Thalaseus sandvicensis (#50783283); Corvus monedula (#50783129); Upupiformes (#50783251); Verongida (#50783207); Neotaenioglossa (#50783242); Oxyrrhinaceae (#50783124); Magnoliophyta (#50783175); Magnoliopsida (#50783174); Pinophyta (#50783234)
[START] [2019-10-14 09:10:20] update_nodes
[STOP] [2019-10-14 09:10:20] update_nodes
[STOP] [2019-10-14 09:10:20] match_nodes
[START] [2019-10-14 09:10:20] reindex_search
[STOP] [2019-10-14 09:10:20] reindex_search
[START] [2019-10-14 09:10:20] normalize_units
[STOP] [2019-10-14 09:10:20] normalize_units
[START] [2019-10-14 09:10:20] calculate_statistics
[STOP] [2019-10-14 09:10:20] calculate_statistics
[START] [2019-10-14 09:10:20] complete_harvest_instance
[START] [2019-10-14 09:10:20] overall_tsv_creation
[INFO] [2019-10-14 09:10:20] Processing group of 282 in 1 batches of 10000
[INFO] [2019-10-14 09:11:05] 99 Traits (unfiltered)...
[INFO] [2019-10-14 09:11:19] 99 Traits (filtered)...
[INFO] [2019-10-14 09:11:19] 0 Associations (filtered)...
[INFO] [2019-10-14 09:11:56] 495 metadata added.
[INFO] [2019-10-14 09:11:56] 0 metadata added.
[INFO] [2019-10-14 09:11:56] Average Time: 74.63
[INFO] [2019-10-14 09:11:56] Total Time: 1m36s
[STOP] [2019-10-14 09:11:56] overall_tsv_creation
[INFO] [2019-10-14 09:11:56] Done. Check your files:
[INFO] [2019-10-14 09:11:56] (282 lines) /app/public/data/monaco_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 09:11:56] (1283 lines) /app/public/data/monaco_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 09:11:56] (282 lines) /app/public/data/monaco_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 09:11:56] (100 lines) /app/public/data/monaco_sp_list/publish_traits.tsv
[INFO] [2019-10-14 09:11:56] (496 lines) /app/public/data/monaco_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 09:11:56] complete_harvest_instance
[START] [2019-10-14 09:11:56] completed
[STOP] [2019-10-14 09:11:56] completed
[STOP] [2019-10-14 09:11:56] logged process, took 134.39

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