Harvest for Liechtenstein Species List Created 14 Oct 02:03

Stage: completed
Fetched: 14 Oct 02:03
Validated: 14 Oct 02:03
Deltas Created 14 Oct 02:03
Units Normalized: 14 Oct 02:06
Ancestry Built: 14 Oct 02:03
Nodes Matched: 14 Oct 02:05
Names Parsed: 14 Oct 02:04
New Models Stored: 14 Oct 02:03
Indexed: 14 Oct 02:06
Completed: 14 Oct 02:07
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 02:03:26 -0400 by logger.rb/56815
[START] [2019-10-14 02:03:26] logged process
[START] [2019-10-14 02:03:26] create_harvest_instance
[STOP] [2019-10-14 02:03:27] create_harvest_instance
[START] [2019-10-14 02:03:27] fetch_files
[STOP] [2019-10-14 02:03:27] fetch_files
[START] [2019-10-14 02:03:27] validate_each_file
[STOP] [2019-10-14 02:03:27] validate_each_file
[START] [2019-10-14 02:03:27] convert_to_csv
[CMD] [2019-10-14 02:03:27] /usr/bin/sort /app/public/converted_csv/liechtenstein_sp_refs_16411.csv > /app/public/converted_csv/liechtenstein_sp_refs_16411.csv_sorted
[CMD] [2019-10-14 02:03:27] /usr/bin/sort /app/public/converted_csv/liechtenstein_sp_nodes_16412.csv > /app/public/converted_csv/liechtenstein_sp_nodes_16412.csv_sorted
[CMD] [2019-10-14 02:03:28] /usr/bin/sort /app/public/converted_csv/liechtenstein_sp_occurrences_16413.csv > /app/public/converted_csv/liechtenstein_sp_occurrences_16413.csv_sorted
[CMD] [2019-10-14 02:03:28] /usr/bin/sort /app/public/converted_csv/liechtenstein_sp_measurements_16414.csv > /app/public/converted_csv/liechtenstein_sp_measurements_16414.csv_sorted
[STOP] [2019-10-14 02:03:28] convert_to_csv
[START] [2019-10-14 02:03:28] calculate_delta
[CMD] [2019-10-14 02:03:28] echo "0a" > /app/public/diff/liechtenstein_sp_refs_16411.diff
[CMD] [2019-10-14 02:03:28] tail -n +1 /app/public/converted_csv/liechtenstein_sp_refs_16411.csv >> /app/public/diff/liechtenstein_sp_refs_16411.diff
[CMD] [2019-10-14 02:03:28] echo "." >> /app/public/diff/liechtenstein_sp_refs_16411.diff
[CMD] [2019-10-14 02:03:28] echo "0a" > /app/public/diff/liechtenstein_sp_nodes_16412.diff
[CMD] [2019-10-14 02:03:28] tail -n +1 /app/public/converted_csv/liechtenstein_sp_nodes_16412.csv >> /app/public/diff/liechtenstein_sp_nodes_16412.diff
[CMD] [2019-10-14 02:03:28] echo "." >> /app/public/diff/liechtenstein_sp_nodes_16412.diff
[CMD] [2019-10-14 02:03:28] echo "0a" > /app/public/diff/liechtenstein_sp_occurrences_16413.diff
[CMD] [2019-10-14 02:03:28] tail -n +1 /app/public/converted_csv/liechtenstein_sp_occurrences_16413.csv >> /app/public/diff/liechtenstein_sp_occurrences_16413.diff
[CMD] [2019-10-14 02:03:28] echo "." >> /app/public/diff/liechtenstein_sp_occurrences_16413.diff
[CMD] [2019-10-14 02:03:29] echo "0a" > /app/public/diff/liechtenstein_sp_measurements_16414.diff
[CMD] [2019-10-14 02:03:29] tail -n +1 /app/public/converted_csv/liechtenstein_sp_measurements_16414.csv >> /app/public/diff/liechtenstein_sp_measurements_16414.diff
[CMD] [2019-10-14 02:03:29] echo "." >> /app/public/diff/liechtenstein_sp_measurements_16414.diff
[STOP] [2019-10-14 02:03:29] calculate_delta
[START] [2019-10-14 02:03:29] parse_diff_and_store
[INFO] [2019-10-14 02:03:29] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 02:03:29] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 02:03:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 02:03:30] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 02:03:37] Storing 2 References
[INFO] [2019-10-14 02:03:37] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 02:03:37] Average Time: 0.0
[INFO] [2019-10-14 02:03:37] Total Time: 1s
[INFO] [2019-10-14 02:03:37] Storing 2195 ScientificNames
[INFO] [2019-10-14 02:03:37] Processing group of 2195 in 3 groups of 1000
[INFO] [2019-10-14 02:03:38] Average Time: 0.283
[INFO] [2019-10-14 02:03:38] Total Time: 1s
[INFO] [2019-10-14 02:03:38] Storing 2195 Nodes
[INFO] [2019-10-14 02:03:38] Processing group of 2195 in 3 groups of 1000
[INFO] [2019-10-14 02:03:39] Average Time: 0.2
[INFO] [2019-10-14 02:03:39] Total Time: 1s
[INFO] [2019-10-14 02:03:39] Storing 964 Occurrences
[INFO] [2019-10-14 02:03:39] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-14 02:03:39] Average Time: 0.11
[INFO] [2019-10-14 02:03:39] Total Time: 1s
[INFO] [2019-10-14 02:03:39] Storing 2440 TraitsReferences
[INFO] [2019-10-14 02:03:39] Processing group of 2440 in 3 groups of 1000
[INFO] [2019-10-14 02:03:39] Average Time: 0.073
[INFO] [2019-10-14 02:03:39] Total Time: 1s
[INFO] [2019-10-14 02:03:39] Storing 2439 Traits
[INFO] [2019-10-14 02:03:39] Processing group of 2439 in 3 groups of 1000
[INFO] [2019-10-14 02:03:40] Average Time: 0.303
[INFO] [2019-10-14 02:03:40] Total Time: 1s
[INFO] [2019-10-14 02:03:40] Storing 2439 MetaTraits
[INFO] [2019-10-14 02:03:40] Processing group of 2439 in 3 groups of 1000
[INFO] [2019-10-14 02:03:40] Average Time: 0.103
[INFO] [2019-10-14 02:03:40] Total Time: 1s
[STOP] [2019-10-14 02:03:40] parse_diff_and_store
[START] [2019-10-14 02:03:40] resolve_keys
[INFO] [2019-10-14 02:03:52] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 02:03:52] traits to occurrences...
[INFO] [2019-10-14 02:03:53] traits to nodes (through occurrences)...
[INFO] [2019-10-14 02:03:53] Traits to sex term...
[INFO] [2019-10-14 02:03:53] Traits to lifestage term...
[INFO] [2019-10-14 02:03:53] MetaTraits to traits...
[INFO] [2019-10-14 02:03:54] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 02:03:54] Assocs to occurrences...
[INFO] [2019-10-14 02:03:54] Assocs to nodes...
[INFO] [2019-10-14 02:03:54] Assoc to sex term...
[INFO] [2019-10-14 02:03:54] Assoc to lifestage term...
[STOP] [2019-10-14 02:03:54] resolve_keys
[START] [2019-10-14 02:03:54] hold_for_later_1
[STOP] [2019-10-14 02:03:54] hold_for_later_1
[START] [2019-10-14 02:03:54] hold_for_later_2
[STOP] [2019-10-14 02:03:54] hold_for_later_2
[START] [2019-10-14 02:03:54] resolve_missing_parents
[STOP] [2019-10-14 02:03:57] resolve_missing_parents
[START] [2019-10-14 02:03:57] rebuild_nodes
[START] [2019-10-14 02:03:57] Flattener#flatten
[START] [2019-10-14 02:03:57] Flattener#study_resource
[START] [2019-10-14 02:03:57] Flattener#build_ancestry
[STOP] [2019-10-14 02:03:57] Flattener#build_ancestry
[INFO] [2019-10-14 02:03:57] 2195 ancestry keys
[START] [2019-10-14 02:03:57] build_node_ancestors
[INFO] [2019-10-14 02:03:57] old ancestors deleted.
[STOP] [2019-10-14 02:03:58] build_node_ancestors
[START] [2019-10-14 02:03:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 02:03:58] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 02:03:58] Flattener#flatten
[STOP] [2019-10-14 02:03:58] rebuild_nodes
[START] [2019-10-14 02:03:58] resolve_missing_media_owners
[STOP] [2019-10-14 02:03:58] resolve_missing_media_owners
[START] [2019-10-14 02:03:58] sanitize_media_verbatims
[STOP] [2019-10-14 02:03:58] sanitize_media_verbatims
[START] [2019-10-14 02:03:58] queue_downloads
[STOP] [2019-10-14 02:03:58] queue_downloads
[START] [2019-10-14 02:03:58] parse_names
[WARN] [2019-10-14 02:03:58] I see 2195 names which still need to be parsed.
[STOP] [2019-10-14 02:04:01] parse_names
[START] [2019-10-14 02:04:01] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 02:04:01] denormalize_canonical_names_to_nodes
[START] [2019-10-14 02:04:01] match_nodes
[START] [2019-10-14 02:04:01] map_all_nodes_to_pages
[STOP] [2019-10-14 02:05:57] map_all_nodes_to_pages
[INFO] [2019-10-14 02:05:57] 248 Unmatched nodes (of 2195)! That's too many to output. First 10: Aglais io (#50548145); Vanessa cardui (#50548122); Coenonympha glycerion (#50548197); Coenonympha satyrion (#50548326); Coenonympha gardetta (#50549106); Lasiommata (#50548115); Lasiommata megera (#50548114); Lasiommata maera (#50548173); Lasiommata petropolitana (#50548395); Argynnis aglaja (#50548161)
[START] [2019-10-14 02:05:57] update_nodes
[STOP] [2019-10-14 02:05:58] update_nodes
[STOP] [2019-10-14 02:05:58] match_nodes
[START] [2019-10-14 02:05:58] reindex_search
[STOP] [2019-10-14 02:06:02] reindex_search
[START] [2019-10-14 02:06:02] normalize_units
[STOP] [2019-10-14 02:06:02] normalize_units
[START] [2019-10-14 02:06:02] calculate_statistics
[STOP] [2019-10-14 02:06:02] calculate_statistics
[START] [2019-10-14 02:06:02] complete_harvest_instance
[START] [2019-10-14 02:06:02] overall_tsv_creation
[INFO] [2019-10-14 02:06:02] Processing group of 2195 in 1 batches of 10000
[INFO] [2019-10-14 02:06:57] 964 Traits (unfiltered)...
[INFO] [2019-10-14 02:07:11] 964 Traits (filtered)...
[INFO] [2019-10-14 02:07:11] 0 Associations (filtered)...
[INFO] [2019-10-14 02:07:50] 4820 metadata added.
[INFO] [2019-10-14 02:07:50] 0 metadata added.
[INFO] [2019-10-14 02:07:50] Average Time: 84.89
[INFO] [2019-10-14 02:07:50] Total Time: 1m49s
[STOP] [2019-10-14 02:07:50] overall_tsv_creation
[INFO] [2019-10-14 02:07:50] Done. Check your files:
[INFO] [2019-10-14 02:07:50] (2195 lines) /app/public/data/liechtenstein_sp/publish_nodes.tsv
[INFO] [2019-10-14 02:07:51] (3118 lines) /app/public/data/liechtenstein_sp/publish_node_ancestors.tsv
[INFO] [2019-10-14 02:07:51] (2195 lines) /app/public/data/liechtenstein_sp/publish_scientific_names.tsv
[INFO] [2019-10-14 02:07:51] (965 lines) /app/public/data/liechtenstein_sp/publish_traits.tsv
[INFO] [2019-10-14 02:07:51] (4821 lines) /app/public/data/liechtenstein_sp/publish_metadata.tsv
[STOP] [2019-10-14 02:07:51] complete_harvest_instance
[START] [2019-10-14 02:07:51] completed
[STOP] [2019-10-14 02:07:51] completed
[STOP] [2019-10-14 02:07:51] logged process, took 264.37
Latest Process

14 Oct 02:03 EXITED currently processing 0