Harvest for Libya Species List Created 14 Oct 01:59

Stage: completed
Fetched: 14 Oct 01:59
Validated: 14 Oct 01:59
Deltas Created 14 Oct 01:59
Units Normalized: 14 Oct 02:01
Ancestry Built: 14 Oct 01:59
Nodes Matched: 14 Oct 02:01
Names Parsed: 14 Oct 01:59
New Models Stored: 14 Oct 01:59
Indexed: 14 Oct 02:01
Completed: 14 Oct 02:03
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 01:59:00 -0400 by logger.rb/56815
[START] [2019-10-14 01:59:00] logged process
[START] [2019-10-14 01:59:00] create_harvest_instance
[STOP] [2019-10-14 01:59:00] create_harvest_instance
[START] [2019-10-14 01:59:00] fetch_files
[STOP] [2019-10-14 01:59:00] fetch_files
[START] [2019-10-14 01:59:00] validate_each_file
[STOP] [2019-10-14 01:59:01] validate_each_file
[START] [2019-10-14 01:59:01] convert_to_csv
[CMD] [2019-10-14 01:59:01] /usr/bin/sort /app/public/converted_csv/libya_sp_list_refs_16403.csv > /app/public/converted_csv/libya_sp_list_refs_16403.csv_sorted
[CMD] [2019-10-14 01:59:01] /usr/bin/sort /app/public/converted_csv/libya_sp_list_nodes_16404.csv > /app/public/converted_csv/libya_sp_list_nodes_16404.csv_sorted
[CMD] [2019-10-14 01:59:01] /usr/bin/sort /app/public/converted_csv/libya_sp_list_occurrences_16405.csv > /app/public/converted_csv/libya_sp_list_occurrences_16405.csv_sorted
[CMD] [2019-10-14 01:59:01] /usr/bin/sort /app/public/converted_csv/libya_sp_list_measurements_16406.csv > /app/public/converted_csv/libya_sp_list_measurements_16406.csv_sorted
[STOP] [2019-10-14 01:59:01] convert_to_csv
[START] [2019-10-14 01:59:01] calculate_delta
[CMD] [2019-10-14 01:59:01] echo "0a" > /app/public/diff/libya_sp_list_refs_16403.diff
[CMD] [2019-10-14 01:59:01] tail -n +1 /app/public/converted_csv/libya_sp_list_refs_16403.csv >> /app/public/diff/libya_sp_list_refs_16403.diff
[CMD] [2019-10-14 01:59:01] echo "." >> /app/public/diff/libya_sp_list_refs_16403.diff
[CMD] [2019-10-14 01:59:01] echo "0a" > /app/public/diff/libya_sp_list_nodes_16404.diff
[CMD] [2019-10-14 01:59:01] tail -n +1 /app/public/converted_csv/libya_sp_list_nodes_16404.csv >> /app/public/diff/libya_sp_list_nodes_16404.diff
[CMD] [2019-10-14 01:59:02] echo "." >> /app/public/diff/libya_sp_list_nodes_16404.diff
[CMD] [2019-10-14 01:59:02] echo "0a" > /app/public/diff/libya_sp_list_occurrences_16405.diff
[CMD] [2019-10-14 01:59:02] tail -n +1 /app/public/converted_csv/libya_sp_list_occurrences_16405.csv >> /app/public/diff/libya_sp_list_occurrences_16405.diff
[CMD] [2019-10-14 01:59:02] echo "." >> /app/public/diff/libya_sp_list_occurrences_16405.diff
[CMD] [2019-10-14 01:59:02] echo "0a" > /app/public/diff/libya_sp_list_measurements_16406.diff
[CMD] [2019-10-14 01:59:02] tail -n +1 /app/public/converted_csv/libya_sp_list_measurements_16406.csv >> /app/public/diff/libya_sp_list_measurements_16406.diff
[CMD] [2019-10-14 01:59:02] echo "." >> /app/public/diff/libya_sp_list_measurements_16406.diff
[STOP] [2019-10-14 01:59:02] calculate_delta
[START] [2019-10-14 01:59:02] parse_diff_and_store
[INFO] [2019-10-14 01:59:02] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 01:59:02] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 01:59:03] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 01:59:04] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 01:59:09] Storing 2 References
[INFO] [2019-10-14 01:59:09] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 01:59:09] Average Time: 0.0
[INFO] [2019-10-14 01:59:09] Total Time: 1s
[INFO] [2019-10-14 01:59:09] Storing 1996 ScientificNames
[INFO] [2019-10-14 01:59:09] Processing group of 1996 in 2 groups of 1000
[INFO] [2019-10-14 01:59:10] Average Time: 0.475
[INFO] [2019-10-14 01:59:10] Total Time: 1s
[INFO] [2019-10-14 01:59:10] Storing 1996 Nodes
[INFO] [2019-10-14 01:59:10] Processing group of 1996 in 2 groups of 1000
[INFO] [2019-10-14 01:59:11] Average Time: 0.295
[INFO] [2019-10-14 01:59:11] Total Time: 1s
[INFO] [2019-10-14 01:59:11] Storing 964 Occurrences
[INFO] [2019-10-14 01:59:11] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-14 01:59:11] Average Time: 0.12
[INFO] [2019-10-14 01:59:11] Total Time: 1s
[INFO] [2019-10-14 01:59:11] Storing 1970 TraitsReferences
[INFO] [2019-10-14 01:59:11] Processing group of 1970 in 2 groups of 1000
[INFO] [2019-10-14 01:59:11] Average Time: 0.11
[INFO] [2019-10-14 01:59:11] Total Time: 1s
[INFO] [2019-10-14 01:59:11] Storing 1969 Traits
[INFO] [2019-10-14 01:59:11] Processing group of 1969 in 2 groups of 1000
[INFO] [2019-10-14 01:59:12] Average Time: 0.34
[INFO] [2019-10-14 01:59:12] Total Time: 1s
[INFO] [2019-10-14 01:59:12] Storing 1969 MetaTraits
[INFO] [2019-10-14 01:59:12] Processing group of 1969 in 2 groups of 1000
[INFO] [2019-10-14 01:59:12] Average Time: 0.13
[INFO] [2019-10-14 01:59:12] Total Time: 1s
[STOP] [2019-10-14 01:59:12] parse_diff_and_store
[START] [2019-10-14 01:59:12] resolve_keys
[INFO] [2019-10-14 01:59:22] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 01:59:23] traits to occurrences...
[INFO] [2019-10-14 01:59:24] traits to nodes (through occurrences)...
[INFO] [2019-10-14 01:59:24] Traits to sex term...
[INFO] [2019-10-14 01:59:24] Traits to lifestage term...
[INFO] [2019-10-14 01:59:25] MetaTraits to traits...
[INFO] [2019-10-14 01:59:25] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 01:59:25] Assocs to occurrences...
[INFO] [2019-10-14 01:59:25] Assocs to nodes...
[INFO] [2019-10-14 01:59:25] Assoc to sex term...
[INFO] [2019-10-14 01:59:25] Assoc to lifestage term...
[STOP] [2019-10-14 01:59:25] resolve_keys
[START] [2019-10-14 01:59:25] hold_for_later_1
[STOP] [2019-10-14 01:59:25] hold_for_later_1
[START] [2019-10-14 01:59:25] hold_for_later_2
[STOP] [2019-10-14 01:59:25] hold_for_later_2
[START] [2019-10-14 01:59:25] resolve_missing_parents
[STOP] [2019-10-14 01:59:28] resolve_missing_parents
[START] [2019-10-14 01:59:28] rebuild_nodes
[START] [2019-10-14 01:59:28] Flattener#flatten
[START] [2019-10-14 01:59:28] Flattener#study_resource
[START] [2019-10-14 01:59:28] Flattener#build_ancestry
[STOP] [2019-10-14 01:59:28] Flattener#build_ancestry
[INFO] [2019-10-14 01:59:28] 1996 ancestry keys
[START] [2019-10-14 01:59:28] build_node_ancestors
[INFO] [2019-10-14 01:59:28] old ancestors deleted.
[STOP] [2019-10-14 01:59:28] build_node_ancestors
[START] [2019-10-14 01:59:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:59:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 01:59:28] Flattener#flatten
[STOP] [2019-10-14 01:59:28] rebuild_nodes
[START] [2019-10-14 01:59:28] resolve_missing_media_owners
[STOP] [2019-10-14 01:59:28] resolve_missing_media_owners
[START] [2019-10-14 01:59:28] sanitize_media_verbatims
[STOP] [2019-10-14 01:59:28] sanitize_media_verbatims
[START] [2019-10-14 01:59:28] queue_downloads
[STOP] [2019-10-14 01:59:28] queue_downloads
[START] [2019-10-14 01:59:28] parse_names
[WARN] [2019-10-14 01:59:28] I see 1996 names which still need to be parsed.
[STOP] [2019-10-14 01:59:31] parse_names
[START] [2019-10-14 01:59:31] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 01:59:31] denormalize_canonical_names_to_nodes
[START] [2019-10-14 01:59:31] match_nodes
[START] [2019-10-14 01:59:31] map_all_nodes_to_pages
[STOP] [2019-10-14 02:01:28] map_all_nodes_to_pages
[INFO] [2019-10-14 02:01:28] 194 Unmatched nodes (of 1996)! That's too many to output. First 10: Vulpiella letourneuxii (#50547552); Pennisetum (#50547033); Myocricetodon (#50547611); Myocricetodon cherifiensis (#50547610); Calandrella rufescens (#50546706); Callerya congestiflora (#50546537); Ohwia caudatum (#50546674); Cercis gigantea (#50546688); Streptopelia senegalensis (#50546096); Carduelis cannabina (#50546244)
[START] [2019-10-14 02:01:28] update_nodes
[STOP] [2019-10-14 02:01:29] update_nodes
[STOP] [2019-10-14 02:01:29] match_nodes
[START] [2019-10-14 02:01:29] reindex_search
[STOP] [2019-10-14 02:01:34] reindex_search
[START] [2019-10-14 02:01:34] normalize_units
[STOP] [2019-10-14 02:01:34] normalize_units
[START] [2019-10-14 02:01:34] calculate_statistics
[STOP] [2019-10-14 02:01:34] calculate_statistics
[START] [2019-10-14 02:01:34] complete_harvest_instance
[START] [2019-10-14 02:01:34] overall_tsv_creation
[INFO] [2019-10-14 02:01:34] Processing group of 1996 in 1 batches of 10000
[INFO] [2019-10-14 02:02:28] 964 Traits (unfiltered)...
[INFO] [2019-10-14 02:02:41] 964 Traits (filtered)...
[INFO] [2019-10-14 02:02:41] 0 Associations (filtered)...
[INFO] [2019-10-14 02:03:22] 4819 metadata added.
[INFO] [2019-10-14 02:03:22] 0 metadata added.
[INFO] [2019-10-14 02:03:22] Average Time: 86.06
[INFO] [2019-10-14 02:03:22] Total Time: 1m48s
[STOP] [2019-10-14 02:03:22] overall_tsv_creation
[INFO] [2019-10-14 02:03:22] Done. Check your files:
[INFO] [2019-10-14 02:03:22] (1996 lines) /app/public/data/libya_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 02:03:22] (2612 lines) /app/public/data/libya_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 02:03:23] (1996 lines) /app/public/data/libya_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 02:03:23] (965 lines) /app/public/data/libya_sp_list/publish_traits.tsv
[INFO] [2019-10-14 02:03:23] (4820 lines) /app/public/data/libya_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 02:03:23] complete_harvest_instance
[START] [2019-10-14 02:03:23] completed
[STOP] [2019-10-14 02:03:23] completed
[STOP] [2019-10-14 02:03:23] logged process, took 262.99
Latest Process

14 Oct 01:59 EXITED currently processing 0