Harvest for Kosovo Species List Created 14 Oct 00:37

Stage: completed
Fetched: 14 Oct 00:37
Validated: 14 Oct 00:37
Deltas Created 14 Oct 00:37
Units Normalized: 14 Oct 00:40
Ancestry Built: 14 Oct 00:38
Nodes Matched: 14 Oct 00:39
Names Parsed: 14 Oct 00:38
New Models Stored: 14 Oct 00:38
Indexed: 14 Oct 00:40
Completed: 14 Oct 00:41
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-14 00:37:52 -0400 by logger.rb/56815
[START] [2019-10-14 00:37:52] logged process
[START] [2019-10-14 00:37:52] create_harvest_instance
[STOP] [2019-10-14 00:37:53] create_harvest_instance
[START] [2019-10-14 00:37:53] fetch_files
[STOP] [2019-10-14 00:37:53] fetch_files
[START] [2019-10-14 00:37:53] validate_each_file
[STOP] [2019-10-14 00:37:53] validate_each_file
[START] [2019-10-14 00:37:53] convert_to_csv
[CMD] [2019-10-14 00:37:53] /usr/bin/sort /app/public/converted_csv/kosovo_sp_list_refs_16315.csv > /app/public/converted_csv/kosovo_sp_list_refs_16315.csv_sorted
[CMD] [2019-10-14 00:37:53] /usr/bin/sort /app/public/converted_csv/kosovo_sp_list_nodes_16316.csv > /app/public/converted_csv/kosovo_sp_list_nodes_16316.csv_sorted
[CMD] [2019-10-14 00:37:53] /usr/bin/sort /app/public/converted_csv/kosovo_sp_list_occurrences_16317.csv > /app/public/converted_csv/kosovo_sp_list_occurrences_16317.csv_sorted
[CMD] [2019-10-14 00:37:53] /usr/bin/sort /app/public/converted_csv/kosovo_sp_list_measurements_16318.csv > /app/public/converted_csv/kosovo_sp_list_measurements_16318.csv_sorted
[STOP] [2019-10-14 00:37:54] convert_to_csv
[START] [2019-10-14 00:37:54] calculate_delta
[CMD] [2019-10-14 00:37:54] echo "0a" > /app/public/diff/kosovo_sp_list_refs_16315.diff
[CMD] [2019-10-14 00:37:54] tail -n +1 /app/public/converted_csv/kosovo_sp_list_refs_16315.csv >> /app/public/diff/kosovo_sp_list_refs_16315.diff
[CMD] [2019-10-14 00:37:54] echo "." >> /app/public/diff/kosovo_sp_list_refs_16315.diff
[CMD] [2019-10-14 00:37:54] echo "0a" > /app/public/diff/kosovo_sp_list_nodes_16316.diff
[CMD] [2019-10-14 00:37:54] tail -n +1 /app/public/converted_csv/kosovo_sp_list_nodes_16316.csv >> /app/public/diff/kosovo_sp_list_nodes_16316.diff
[CMD] [2019-10-14 00:37:54] echo "." >> /app/public/diff/kosovo_sp_list_nodes_16316.diff
[CMD] [2019-10-14 00:37:54] echo "0a" > /app/public/diff/kosovo_sp_list_occurrences_16317.diff
[CMD] [2019-10-14 00:37:54] tail -n +1 /app/public/converted_csv/kosovo_sp_list_occurrences_16317.csv >> /app/public/diff/kosovo_sp_list_occurrences_16317.diff
[CMD] [2019-10-14 00:37:54] echo "." >> /app/public/diff/kosovo_sp_list_occurrences_16317.diff
[CMD] [2019-10-14 00:37:54] echo "0a" > /app/public/diff/kosovo_sp_list_measurements_16318.diff
[CMD] [2019-10-14 00:37:54] tail -n +1 /app/public/converted_csv/kosovo_sp_list_measurements_16318.csv >> /app/public/diff/kosovo_sp_list_measurements_16318.diff
[CMD] [2019-10-14 00:37:55] echo "." >> /app/public/diff/kosovo_sp_list_measurements_16318.diff
[STOP] [2019-10-14 00:37:55] calculate_delta
[START] [2019-10-14 00:37:55] parse_diff_and_store
[INFO] [2019-10-14 00:37:55] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 00:37:55] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 00:37:56] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 00:37:56] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 00:38:00] Storing 2 References
[INFO] [2019-10-14 00:38:00] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 00:38:00] Average Time: 0.0
[INFO] [2019-10-14 00:38:00] Total Time: 1s
[INFO] [2019-10-14 00:38:00] Storing 1567 ScientificNames
[INFO] [2019-10-14 00:38:00] Processing group of 1567 in 2 groups of 1000
[INFO] [2019-10-14 00:38:01] Average Time: 0.335
[INFO] [2019-10-14 00:38:01] Total Time: 1s
[INFO] [2019-10-14 00:38:01] Storing 1567 Nodes
[INFO] [2019-10-14 00:38:01] Processing group of 1567 in 2 groups of 1000
[INFO] [2019-10-14 00:38:01] Average Time: 0.25
[INFO] [2019-10-14 00:38:01] Total Time: 1s
[INFO] [2019-10-14 00:38:01] Storing 482 Occurrences
[INFO] [2019-10-14 00:38:01] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-14 00:38:01] Average Time: 0.07
[INFO] [2019-10-14 00:38:01] Total Time: 1s
[INFO] [2019-10-14 00:38:01] Storing 1530 TraitsReferences
[INFO] [2019-10-14 00:38:01] Processing group of 1530 in 2 groups of 1000
[INFO] [2019-10-14 00:38:02] Average Time: 0.1
[INFO] [2019-10-14 00:38:02] Total Time: 1s
[INFO] [2019-10-14 00:38:02] Storing 1529 Traits
[INFO] [2019-10-14 00:38:02] Processing group of 1529 in 2 groups of 1000
[INFO] [2019-10-14 00:38:02] Average Time: 0.3
[INFO] [2019-10-14 00:38:02] Total Time: 1s
[INFO] [2019-10-14 00:38:02] Storing 1530 MetaTraits
[INFO] [2019-10-14 00:38:02] Processing group of 1530 in 2 groups of 1000
[INFO] [2019-10-14 00:38:03] Average Time: 0.105
[INFO] [2019-10-14 00:38:03] Total Time: 1s
[STOP] [2019-10-14 00:38:03] parse_diff_and_store
[START] [2019-10-14 00:38:03] resolve_keys
[INFO] [2019-10-14 00:38:11] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 00:38:11] traits to occurrences...
[INFO] [2019-10-14 00:38:12] traits to nodes (through occurrences)...
[INFO] [2019-10-14 00:38:12] Traits to sex term...
[INFO] [2019-10-14 00:38:12] Traits to lifestage term...
[INFO] [2019-10-14 00:38:13] MetaTraits to traits...
[INFO] [2019-10-14 00:38:13] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 00:38:13] Assocs to occurrences...
[INFO] [2019-10-14 00:38:13] Assocs to nodes...
[INFO] [2019-10-14 00:38:13] Assoc to sex term...
[INFO] [2019-10-14 00:38:13] Assoc to lifestage term...
[STOP] [2019-10-14 00:38:13] resolve_keys
[START] [2019-10-14 00:38:13] hold_for_later_1
[STOP] [2019-10-14 00:38:13] hold_for_later_1
[START] [2019-10-14 00:38:13] hold_for_later_2
[STOP] [2019-10-14 00:38:13] hold_for_later_2
[START] [2019-10-14 00:38:13] resolve_missing_parents
[STOP] [2019-10-14 00:38:15] resolve_missing_parents
[START] [2019-10-14 00:38:15] rebuild_nodes
[START] [2019-10-14 00:38:15] Flattener#flatten
[START] [2019-10-14 00:38:15] Flattener#study_resource
[START] [2019-10-14 00:38:15] Flattener#build_ancestry
[STOP] [2019-10-14 00:38:15] Flattener#build_ancestry
[INFO] [2019-10-14 00:38:15] 1567 ancestry keys
[START] [2019-10-14 00:38:15] build_node_ancestors
[INFO] [2019-10-14 00:38:15] old ancestors deleted.
[STOP] [2019-10-14 00:38:16] build_node_ancestors
[START] [2019-10-14 00:38:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:38:16] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 00:38:16] Flattener#flatten
[STOP] [2019-10-14 00:38:16] rebuild_nodes
[START] [2019-10-14 00:38:16] resolve_missing_media_owners
[STOP] [2019-10-14 00:38:16] resolve_missing_media_owners
[START] [2019-10-14 00:38:16] sanitize_media_verbatims
[STOP] [2019-10-14 00:38:16] sanitize_media_verbatims
[START] [2019-10-14 00:38:16] queue_downloads
[STOP] [2019-10-14 00:38:16] queue_downloads
[START] [2019-10-14 00:38:16] parse_names
[WARN] [2019-10-14 00:38:16] I see 1567 names which still need to be parsed.
[STOP] [2019-10-14 00:38:18] parse_names
[START] [2019-10-14 00:38:18] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 00:38:18] denormalize_canonical_names_to_nodes
[START] [2019-10-14 00:38:18] match_nodes
[START] [2019-10-14 00:38:18] map_all_nodes_to_pages
[STOP] [2019-10-14 00:39:57] map_all_nodes_to_pages
[INFO] [2019-10-14 00:39:57] 109 Unmatched nodes (of 1567)! That's too many to output. First 10: Alliaceae (#50506805); Corvus monedula (#50506540); Parus caeruleus (#50507308); Parus palustris (#50507494); Delichon urbica (#50506826); Carduelis chloris (#50506833); Dendrocopos medius (#50506333); Dendrocopos minor (#50506928); Anas querquedula (#50507248); Bonasa bonasia (#50506786)
[START] [2019-10-14 00:39:57] update_nodes
[STOP] [2019-10-14 00:39:58] update_nodes
[STOP] [2019-10-14 00:39:58] match_nodes
[START] [2019-10-14 00:39:58] reindex_search
[STOP] [2019-10-14 00:40:01] reindex_search
[START] [2019-10-14 00:40:01] normalize_units
[STOP] [2019-10-14 00:40:01] normalize_units
[START] [2019-10-14 00:40:01] calculate_statistics
[STOP] [2019-10-14 00:40:01] calculate_statistics
[START] [2019-10-14 00:40:01] complete_harvest_instance
[START] [2019-10-14 00:40:01] overall_tsv_creation
[INFO] [2019-10-14 00:40:01] Processing group of 1567 in 1 batches of 10000
[INFO] [2019-10-14 00:40:53] 482 Traits (unfiltered)...
[INFO] [2019-10-14 00:41:06] 482 Traits (filtered)...
[INFO] [2019-10-14 00:41:06] 0 Associations (filtered)...
[INFO] [2019-10-14 00:41:45] 2410 metadata added.
[INFO] [2019-10-14 00:41:45] 0 metadata added.
[INFO] [2019-10-14 00:41:45] Average Time: 82.53
[INFO] [2019-10-14 00:41:45] Total Time: 1m45s
[STOP] [2019-10-14 00:41:45] overall_tsv_creation
[INFO] [2019-10-14 00:41:45] Done. Check your files:
[INFO] [2019-10-14 00:41:45] (1567 lines) /app/public/data/kosovo_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 00:41:46] (4886 lines) /app/public/data/kosovo_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 00:41:46] (1567 lines) /app/public/data/kosovo_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 00:41:46] (483 lines) /app/public/data/kosovo_sp_list/publish_traits.tsv
[INFO] [2019-10-14 00:41:46] (2411 lines) /app/public/data/kosovo_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 00:41:46] complete_harvest_instance
[START] [2019-10-14 00:41:46] completed
[STOP] [2019-10-14 00:41:46] completed
[STOP] [2019-10-14 00:41:46] logged process, took 233.47
Latest Process

14 Oct 00:37 EXITED currently processing 0