Harvest for Comoros Species List Created 12 Oct 06:59

Stage: completed
Fetched: 12 Oct 06:59
Validated: 12 Oct 06:59
Deltas Created 12 Oct 06:59
Units Normalized: 12 Oct 07:01
Ancestry Built: 12 Oct 06:59
Nodes Matched: 12 Oct 07:01
Names Parsed: 12 Oct 06:59
New Models Stored: 12 Oct 06:59
Indexed: 12 Oct 07:01
Completed: 12 Oct 07:03
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 06:59:25 -0400 by logger.rb/56815
[START] [2019-10-12 06:59:25] logged process
[START] [2019-10-12 06:59:25] create_harvest_instance
[STOP] [2019-10-12 06:59:26] create_harvest_instance
[START] [2019-10-12 06:59:26] fetch_files
[STOP] [2019-10-12 06:59:26] fetch_files
[START] [2019-10-12 06:59:26] validate_each_file
[STOP] [2019-10-12 06:59:26] validate_each_file
[START] [2019-10-12 06:59:26] convert_to_csv
[CMD] [2019-10-12 06:59:26] /usr/bin/sort /app/public/converted_csv/comoros_sp_list_refs_15459.csv > /app/public/converted_csv/comoros_sp_list_refs_15459.csv_sorted
[CMD] [2019-10-12 06:59:26] /usr/bin/sort /app/public/converted_csv/comoros_sp_list_nodes_15460.csv > /app/public/converted_csv/comoros_sp_list_nodes_15460.csv_sorted
[CMD] [2019-10-12 06:59:26] /usr/bin/sort /app/public/converted_csv/comoros_sp_list_occurrences_15461.csv > /app/public/converted_csv/comoros_sp_list_occurrences_15461.csv_sorted
[CMD] [2019-10-12 06:59:26] /usr/bin/sort /app/public/converted_csv/comoros_sp_list_measurements_15462.csv > /app/public/converted_csv/comoros_sp_list_measurements_15462.csv_sorted
[STOP] [2019-10-12 06:59:26] convert_to_csv
[START] [2019-10-12 06:59:26] calculate_delta
[CMD] [2019-10-12 06:59:26] echo "0a" > /app/public/diff/comoros_sp_list_refs_15459.diff
[CMD] [2019-10-12 06:59:26] tail -n +1 /app/public/converted_csv/comoros_sp_list_refs_15459.csv >> /app/public/diff/comoros_sp_list_refs_15459.diff
[CMD] [2019-10-12 06:59:26] echo "." >> /app/public/diff/comoros_sp_list_refs_15459.diff
[CMD] [2019-10-12 06:59:27] echo "0a" > /app/public/diff/comoros_sp_list_nodes_15460.diff
[CMD] [2019-10-12 06:59:27] tail -n +1 /app/public/converted_csv/comoros_sp_list_nodes_15460.csv >> /app/public/diff/comoros_sp_list_nodes_15460.diff
[CMD] [2019-10-12 06:59:27] echo "." >> /app/public/diff/comoros_sp_list_nodes_15460.diff
[CMD] [2019-10-12 06:59:27] echo "0a" > /app/public/diff/comoros_sp_list_occurrences_15461.diff
[CMD] [2019-10-12 06:59:27] tail -n +1 /app/public/converted_csv/comoros_sp_list_occurrences_15461.csv >> /app/public/diff/comoros_sp_list_occurrences_15461.diff
[CMD] [2019-10-12 06:59:27] echo "." >> /app/public/diff/comoros_sp_list_occurrences_15461.diff
[CMD] [2019-10-12 06:59:27] echo "0a" > /app/public/diff/comoros_sp_list_measurements_15462.diff
[CMD] [2019-10-12 06:59:27] tail -n +1 /app/public/converted_csv/comoros_sp_list_measurements_15462.csv >> /app/public/diff/comoros_sp_list_measurements_15462.diff
[CMD] [2019-10-12 06:59:27] echo "." >> /app/public/diff/comoros_sp_list_measurements_15462.diff
[STOP] [2019-10-12 06:59:27] calculate_delta
[START] [2019-10-12 06:59:27] parse_diff_and_store
[INFO] [2019-10-12 06:59:27] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 06:59:28] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 06:59:28] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 06:59:29] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 06:59:35] Storing 2 References
[INFO] [2019-10-12 06:59:35] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 06:59:35] Average Time: 0.0
[INFO] [2019-10-12 06:59:35] Total Time: 1s
[INFO] [2019-10-12 06:59:35] Storing 2110 ScientificNames
[INFO] [2019-10-12 06:59:35] Processing group of 2110 in 3 groups of 1000
[INFO] [2019-10-12 06:59:36] Average Time: 0.25
[INFO] [2019-10-12 06:59:36] Total Time: 1s
[INFO] [2019-10-12 06:59:36] Storing 2110 Nodes
[INFO] [2019-10-12 06:59:36] Processing group of 2110 in 3 groups of 1000
[INFO] [2019-10-12 06:59:37] Average Time: 0.267
[INFO] [2019-10-12 06:59:37] Total Time: 1s
[INFO] [2019-10-12 06:59:37] Storing 964 Occurrences
[INFO] [2019-10-12 06:59:37] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-12 06:59:37] Average Time: 0.13
[INFO] [2019-10-12 06:59:37] Total Time: 1s
[INFO] [2019-10-12 06:59:37] Storing 2288 TraitsReferences
[INFO] [2019-10-12 06:59:37] Processing group of 2288 in 3 groups of 1000
[INFO] [2019-10-12 06:59:37] Average Time: 0.08
[INFO] [2019-10-12 06:59:37] Total Time: 1s
[INFO] [2019-10-12 06:59:37] Storing 2287 Traits
[INFO] [2019-10-12 06:59:37] Processing group of 2287 in 3 groups of 1000
[INFO] [2019-10-12 06:59:38] Average Time: 0.263
[INFO] [2019-10-12 06:59:38] Total Time: 1s
[INFO] [2019-10-12 06:59:38] Storing 2288 MetaTraits
[INFO] [2019-10-12 06:59:38] Processing group of 2288 in 3 groups of 1000
[INFO] [2019-10-12 06:59:39] Average Time: 0.103
[INFO] [2019-10-12 06:59:39] Total Time: 1s
[STOP] [2019-10-12 06:59:39] parse_diff_and_store
[START] [2019-10-12 06:59:39] resolve_keys
[INFO] [2019-10-12 06:59:49] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 06:59:50] traits to occurrences...
[INFO] [2019-10-12 06:59:51] traits to nodes (through occurrences)...
[INFO] [2019-10-12 06:59:51] Traits to sex term...
[INFO] [2019-10-12 06:59:51] Traits to lifestage term...
[INFO] [2019-10-12 06:59:51] MetaTraits to traits...
[INFO] [2019-10-12 06:59:51] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 06:59:51] Assocs to occurrences...
[INFO] [2019-10-12 06:59:51] Assocs to nodes...
[INFO] [2019-10-12 06:59:51] Assoc to sex term...
[INFO] [2019-10-12 06:59:51] Assoc to lifestage term...
[STOP] [2019-10-12 06:59:51] resolve_keys
[START] [2019-10-12 06:59:51] hold_for_later_1
[STOP] [2019-10-12 06:59:51] hold_for_later_1
[START] [2019-10-12 06:59:51] hold_for_later_2
[STOP] [2019-10-12 06:59:51] hold_for_later_2
[START] [2019-10-12 06:59:51] resolve_missing_parents
[STOP] [2019-10-12 06:59:55] resolve_missing_parents
[START] [2019-10-12 06:59:55] rebuild_nodes
[START] [2019-10-12 06:59:55] Flattener#flatten
[START] [2019-10-12 06:59:55] Flattener#study_resource
[START] [2019-10-12 06:59:55] Flattener#build_ancestry
[STOP] [2019-10-12 06:59:55] Flattener#build_ancestry
[INFO] [2019-10-12 06:59:55] 2110 ancestry keys
[START] [2019-10-12 06:59:55] build_node_ancestors
[INFO] [2019-10-12 06:59:55] old ancestors deleted.
[STOP] [2019-10-12 06:59:55] build_node_ancestors
[START] [2019-10-12 06:59:55] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 06:59:55] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 06:59:55] Flattener#flatten
[STOP] [2019-10-12 06:59:55] rebuild_nodes
[START] [2019-10-12 06:59:55] resolve_missing_media_owners
[STOP] [2019-10-12 06:59:55] resolve_missing_media_owners
[START] [2019-10-12 06:59:55] sanitize_media_verbatims
[STOP] [2019-10-12 06:59:55] sanitize_media_verbatims
[START] [2019-10-12 06:59:55] queue_downloads
[STOP] [2019-10-12 06:59:55] queue_downloads
[START] [2019-10-12 06:59:55] parse_names
[WARN] [2019-10-12 06:59:55] I see 2110 names which still need to be parsed.
[STOP] [2019-10-12 06:59:58] parse_names
[START] [2019-10-12 06:59:58] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 06:59:58] denormalize_canonical_names_to_nodes
[START] [2019-10-12 06:59:58] match_nodes
[START] [2019-10-12 06:59:58] map_all_nodes_to_pages
[STOP] [2019-10-12 07:01:31] map_all_nodes_to_pages
[INFO] [2019-10-12 07:01:31] 80 Unmatched nodes (of 2110)! That's too many to output. First 10: Strumigenys dicomas (#49267612); Strumigenys ludovici (#49267614); Crematogaster tricolor (#49267661); Syllophopsis (#49267664); Syllophopsis cryptobia (#49267663); Pachycondyla wasmanni (#49268124); Technomyrmex docens (#49268944); Streptopelia picturata (#49268324); Gymnothorax grisea (#49269110); Ravenea hildebrandti (#49268696)
[START] [2019-10-12 07:01:31] update_nodes
[STOP] [2019-10-12 07:01:31] update_nodes
[STOP] [2019-10-12 07:01:31] match_nodes
[START] [2019-10-12 07:01:31] reindex_search
[STOP] [2019-10-12 07:01:35] reindex_search
[START] [2019-10-12 07:01:35] normalize_units
[STOP] [2019-10-12 07:01:35] normalize_units
[START] [2019-10-12 07:01:35] calculate_statistics
[STOP] [2019-10-12 07:01:35] calculate_statistics
[START] [2019-10-12 07:01:35] complete_harvest_instance
[START] [2019-10-12 07:01:35] overall_tsv_creation
[INFO] [2019-10-12 07:01:35] Processing group of 2110 in 1 batches of 10000
[INFO] [2019-10-12 07:02:29] 964 Traits (unfiltered)...
[INFO] [2019-10-12 07:02:43] 964 Traits (filtered)...
[INFO] [2019-10-12 07:02:43] 0 Associations (filtered)...
[INFO] [2019-10-12 07:03:21] 4820 metadata added.
[INFO] [2019-10-12 07:03:21] 0 metadata added.
[INFO] [2019-10-12 07:03:21] Average Time: 84.28
[INFO] [2019-10-12 07:03:21] Total Time: 1m47s
[STOP] [2019-10-12 07:03:21] overall_tsv_creation
[INFO] [2019-10-12 07:03:21] Done. Check your files:
[INFO] [2019-10-12 07:03:22] (2110 lines) /app/public/data/comoros_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 07:03:22] (2951 lines) /app/public/data/comoros_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 07:03:22] (2110 lines) /app/public/data/comoros_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 07:03:22] (965 lines) /app/public/data/comoros_sp_list/publish_traits.tsv
[INFO] [2019-10-12 07:03:22] (4821 lines) /app/public/data/comoros_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 07:03:22] complete_harvest_instance
[START] [2019-10-12 07:03:22] completed
[STOP] [2019-10-12 07:03:22] completed
[STOP] [2019-10-12 07:03:22] logged process, took 236.85
Latest Process

12 Oct 06:59 EXITED currently processing 0