Harvest for Mayotte Species List Created 14 Oct 05:36

Stage: completed
Fetched: 14 Oct 05:36
Validated: 14 Oct 05:36
Deltas Created 14 Oct 05:36
Units Normalized: 14 Oct 05:38
Ancestry Built: 14 Oct 05:36
Nodes Matched: 14 Oct 05:38
Names Parsed: 14 Oct 05:36
New Models Stored: 14 Oct 05:36
Indexed: 14 Oct 05:38
Completed: 14 Oct 05:40
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 05:36:01 -0400 by logger.rb/56815
[START] [2019-10-14 05:36:01] logged process
[START] [2019-10-14 05:36:01] create_harvest_instance
[STOP] [2019-10-14 05:36:01] create_harvest_instance
[START] [2019-10-14 05:36:01] fetch_files
[STOP] [2019-10-14 05:36:01] fetch_files
[START] [2019-10-14 05:36:01] validate_each_file
[STOP] [2019-10-14 05:36:02] validate_each_file
[START] [2019-10-14 05:36:02] convert_to_csv
[CMD] [2019-10-14 05:36:02] /usr/bin/sort /app/public/converted_csv/mayotte_sp_list_refs_16571.csv > /app/public/converted_csv/mayotte_sp_list_refs_16571.csv_sorted
[CMD] [2019-10-14 05:36:02] /usr/bin/sort /app/public/converted_csv/mayotte_sp_list_nodes_16572.csv > /app/public/converted_csv/mayotte_sp_list_nodes_16572.csv_sorted
[CMD] [2019-10-14 05:36:02] /usr/bin/sort /app/public/converted_csv/mayotte_sp_list_occurrences_16573.csv > /app/public/converted_csv/mayotte_sp_list_occurrences_16573.csv_sorted
[CMD] [2019-10-14 05:36:02] /usr/bin/sort /app/public/converted_csv/mayotte_sp_list_measurements_16574.csv > /app/public/converted_csv/mayotte_sp_list_measurements_16574.csv_sorted
[STOP] [2019-10-14 05:36:02] convert_to_csv
[START] [2019-10-14 05:36:02] calculate_delta
[CMD] [2019-10-14 05:36:02] echo "0a" > /app/public/diff/mayotte_sp_list_refs_16571.diff
[CMD] [2019-10-14 05:36:02] tail -n +1 /app/public/converted_csv/mayotte_sp_list_refs_16571.csv >> /app/public/diff/mayotte_sp_list_refs_16571.diff
[CMD] [2019-10-14 05:36:02] echo "." >> /app/public/diff/mayotte_sp_list_refs_16571.diff
[CMD] [2019-10-14 05:36:03] echo "0a" > /app/public/diff/mayotte_sp_list_nodes_16572.diff
[CMD] [2019-10-14 05:36:03] tail -n +1 /app/public/converted_csv/mayotte_sp_list_nodes_16572.csv >> /app/public/diff/mayotte_sp_list_nodes_16572.diff
[CMD] [2019-10-14 05:36:03] echo "." >> /app/public/diff/mayotte_sp_list_nodes_16572.diff
[CMD] [2019-10-14 05:36:03] echo "0a" > /app/public/diff/mayotte_sp_list_occurrences_16573.diff
[CMD] [2019-10-14 05:36:03] tail -n +1 /app/public/converted_csv/mayotte_sp_list_occurrences_16573.csv >> /app/public/diff/mayotte_sp_list_occurrences_16573.diff
[CMD] [2019-10-14 05:36:03] echo "." >> /app/public/diff/mayotte_sp_list_occurrences_16573.diff
[CMD] [2019-10-14 05:36:03] echo "0a" > /app/public/diff/mayotte_sp_list_measurements_16574.diff
[CMD] [2019-10-14 05:36:03] tail -n +1 /app/public/converted_csv/mayotte_sp_list_measurements_16574.csv >> /app/public/diff/mayotte_sp_list_measurements_16574.diff
[CMD] [2019-10-14 05:36:03] echo "." >> /app/public/diff/mayotte_sp_list_measurements_16574.diff
[STOP] [2019-10-14 05:36:03] calculate_delta
[START] [2019-10-14 05:36:03] parse_diff_and_store
[INFO] [2019-10-14 05:36:03] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 05:36:04] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 05:36:04] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 05:36:05] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 05:36:11] Storing 2 References
[INFO] [2019-10-14 05:36:11] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 05:36:11] Average Time: 0.0
[INFO] [2019-10-14 05:36:11] Total Time: 1s
[INFO] [2019-10-14 05:36:11] Storing 1935 ScientificNames
[INFO] [2019-10-14 05:36:11] Processing group of 1935 in 2 groups of 1000
[INFO] [2019-10-14 05:36:12] Average Time: 0.41
[INFO] [2019-10-14 05:36:12] Total Time: 1s
[INFO] [2019-10-14 05:36:12] Storing 1935 Nodes
[INFO] [2019-10-14 05:36:12] Processing group of 1935 in 2 groups of 1000
[INFO] [2019-10-14 05:36:12] Average Time: 0.365
[INFO] [2019-10-14 05:36:12] Total Time: 1s
[INFO] [2019-10-14 05:36:12] Storing 964 Occurrences
[INFO] [2019-10-14 05:36:12] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-14 05:36:12] Average Time: 0.12
[INFO] [2019-10-14 05:36:12] Total Time: 1s
[INFO] [2019-10-14 05:36:12] Storing 2050 TraitsReferences
[INFO] [2019-10-14 05:36:12] Processing group of 2050 in 3 groups of 1000
[INFO] [2019-10-14 05:36:13] Average Time: 0.07
[INFO] [2019-10-14 05:36:13] Total Time: 1s
[INFO] [2019-10-14 05:36:13] Storing 2049 Traits
[INFO] [2019-10-14 05:36:13] Processing group of 2049 in 3 groups of 1000
[INFO] [2019-10-14 05:36:13] Average Time: 0.25
[INFO] [2019-10-14 05:36:13] Total Time: 1s
[INFO] [2019-10-14 05:36:13] Storing 2048 MetaTraits
[INFO] [2019-10-14 05:36:13] Processing group of 2048 in 3 groups of 1000
[INFO] [2019-10-14 05:36:14] Average Time: 0.103
[INFO] [2019-10-14 05:36:14] Total Time: 1s
[STOP] [2019-10-14 05:36:14] parse_diff_and_store
[START] [2019-10-14 05:36:14] resolve_keys
[INFO] [2019-10-14 05:36:24] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 05:36:25] traits to occurrences...
[INFO] [2019-10-14 05:36:26] traits to nodes (through occurrences)...
[INFO] [2019-10-14 05:36:26] Traits to sex term...
[INFO] [2019-10-14 05:36:26] Traits to lifestage term...
[INFO] [2019-10-14 05:36:26] MetaTraits to traits...
[INFO] [2019-10-14 05:36:26] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 05:36:27] Assocs to occurrences...
[INFO] [2019-10-14 05:36:27] Assocs to nodes...
[INFO] [2019-10-14 05:36:27] Assoc to sex term...
[INFO] [2019-10-14 05:36:27] Assoc to lifestage term...
[STOP] [2019-10-14 05:36:27] resolve_keys
[START] [2019-10-14 05:36:27] hold_for_later_1
[STOP] [2019-10-14 05:36:27] hold_for_later_1
[START] [2019-10-14 05:36:27] hold_for_later_2
[STOP] [2019-10-14 05:36:27] hold_for_later_2
[START] [2019-10-14 05:36:27] resolve_missing_parents
[STOP] [2019-10-14 05:36:29] resolve_missing_parents
[START] [2019-10-14 05:36:29] rebuild_nodes
[START] [2019-10-14 05:36:29] Flattener#flatten
[START] [2019-10-14 05:36:29] Flattener#study_resource
[START] [2019-10-14 05:36:29] Flattener#build_ancestry
[STOP] [2019-10-14 05:36:29] Flattener#build_ancestry
[INFO] [2019-10-14 05:36:29] 1935 ancestry keys
[START] [2019-10-14 05:36:29] build_node_ancestors
[INFO] [2019-10-14 05:36:29] old ancestors deleted.
[STOP] [2019-10-14 05:36:30] build_node_ancestors
[START] [2019-10-14 05:36:30] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 05:36:30] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 05:36:30] Flattener#flatten
[STOP] [2019-10-14 05:36:30] rebuild_nodes
[START] [2019-10-14 05:36:30] resolve_missing_media_owners
[STOP] [2019-10-14 05:36:30] resolve_missing_media_owners
[START] [2019-10-14 05:36:30] sanitize_media_verbatims
[STOP] [2019-10-14 05:36:30] sanitize_media_verbatims
[START] [2019-10-14 05:36:30] queue_downloads
[STOP] [2019-10-14 05:36:30] queue_downloads
[START] [2019-10-14 05:36:30] parse_names
[WARN] [2019-10-14 05:36:30] I see 1935 names which still need to be parsed.
[STOP] [2019-10-14 05:36:33] parse_names
[START] [2019-10-14 05:36:33] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 05:36:33] denormalize_canonical_names_to_nodes
[START] [2019-10-14 05:36:33] match_nodes
[START] [2019-10-14 05:36:33] map_all_nodes_to_pages
[STOP] [2019-10-14 05:38:13] map_all_nodes_to_pages
[INFO] [2019-10-14 05:38:13] 58 Unmatched nodes (of 1935)! That's too many to output. First 10: Crematogaster tricolor (#50672846); Monomorium micrommaton (#50672911); Strumigenys ludovici (#50672874); Strumigenys emmae (#50672889); Strumigenys dicomas (#50672907); Technomyrmex innocens (#50672887); Technomyrmex pallipes (#50672935); Cardiocondyla minutior (#50672925); Syllophopsis (#50672931); Syllophopsis cryptobia (#50672930)
[START] [2019-10-14 05:38:13] update_nodes
[STOP] [2019-10-14 05:38:14] update_nodes
[STOP] [2019-10-14 05:38:14] match_nodes
[START] [2019-10-14 05:38:14] reindex_search
[STOP] [2019-10-14 05:38:17] reindex_search
[START] [2019-10-14 05:38:17] normalize_units
[STOP] [2019-10-14 05:38:17] normalize_units
[START] [2019-10-14 05:38:17] calculate_statistics
[STOP] [2019-10-14 05:38:17] calculate_statistics
[START] [2019-10-14 05:38:17] complete_harvest_instance
[START] [2019-10-14 05:38:17] overall_tsv_creation
[INFO] [2019-10-14 05:38:17] Processing group of 1935 in 1 batches of 10000
[INFO] [2019-10-14 05:39:10] 964 Traits (unfiltered)...
[INFO] [2019-10-14 05:39:26] 964 Traits (filtered)...
[INFO] [2019-10-14 05:39:26] 0 Associations (filtered)...
[INFO] [2019-10-14 05:40:08] 4818 metadata added.
[INFO] [2019-10-14 05:40:08] 0 metadata added.
[INFO] [2019-10-14 05:40:08] Average Time: 88.27
[INFO] [2019-10-14 05:40:08] Total Time: 1m51s
[STOP] [2019-10-14 05:40:08] overall_tsv_creation
[INFO] [2019-10-14 05:40:08] Done. Check your files:
[INFO] [2019-10-14 05:40:08] (1935 lines) /app/public/data/mayotte_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 05:40:08] (2599 lines) /app/public/data/mayotte_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 05:40:08] (1935 lines) /app/public/data/mayotte_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 05:40:08] (965 lines) /app/public/data/mayotte_sp_list/publish_traits.tsv
[INFO] [2019-10-14 05:40:08] (4819 lines) /app/public/data/mayotte_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 05:40:08] complete_harvest_instance
[START] [2019-10-14 05:40:08] completed
[STOP] [2019-10-14 05:40:08] completed
[STOP] [2019-10-14 05:40:08] logged process, took 247.49
Latest Process

14 Oct 05:36 EXITED currently processing 0