Harvest for Hungary Species List Created 13 Oct 11:17

Stage: completed
Fetched: 13 Oct 11:17
Validated: 13 Oct 11:17
Deltas Created 13 Oct 11:17
Units Normalized: 13 Oct 11:36
Ancestry Built: 13 Oct 11:20
Nodes Matched: 13 Oct 11:35
Names Parsed: 13 Oct 11:20
New Models Stored: 13 Oct 11:18
Indexed: 13 Oct 11:36
Completed: 13 Oct 11:40
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-13 11:17:35 -0400 by logger.rb/56815
[START] [2019-10-13 11:17:35] logged process
[START] [2019-10-13 11:17:36] create_harvest_instance
[STOP] [2019-10-13 11:17:36] create_harvest_instance
[START] [2019-10-13 11:17:36] fetch_files
[STOP] [2019-10-13 11:17:36] fetch_files
[START] [2019-10-13 11:17:36] validate_each_file
[STOP] [2019-10-13 11:17:38] validate_each_file
[START] [2019-10-13 11:17:38] convert_to_csv
[CMD] [2019-10-13 11:17:38] /usr/bin/sort /app/public/converted_csv/hungary_sp_list_refs_16123.csv > /app/public/converted_csv/hungary_sp_list_refs_16123.csv_sorted
[CMD] [2019-10-13 11:17:38] /usr/bin/sort /app/public/converted_csv/hungary_sp_list_nodes_16124.csv > /app/public/converted_csv/hungary_sp_list_nodes_16124.csv_sorted
[CMD] [2019-10-13 11:17:38] /usr/bin/sort /app/public/converted_csv/hungary_sp_list_occurrences_16125.csv > /app/public/converted_csv/hungary_sp_list_occurrences_16125.csv_sorted
[CMD] [2019-10-13 11:17:38] /usr/bin/sort /app/public/converted_csv/hungary_sp_list_measurements_16126.csv > /app/public/converted_csv/hungary_sp_list_measurements_16126.csv_sorted
[STOP] [2019-10-13 11:17:38] convert_to_csv
[START] [2019-10-13 11:17:38] calculate_delta
[CMD] [2019-10-13 11:17:38] echo "0a" > /app/public/diff/hungary_sp_list_refs_16123.diff
[CMD] [2019-10-13 11:17:38] tail -n +1 /app/public/converted_csv/hungary_sp_list_refs_16123.csv >> /app/public/diff/hungary_sp_list_refs_16123.diff
[CMD] [2019-10-13 11:17:38] echo "." >> /app/public/diff/hungary_sp_list_refs_16123.diff
[CMD] [2019-10-13 11:17:38] echo "0a" > /app/public/diff/hungary_sp_list_nodes_16124.diff
[CMD] [2019-10-13 11:17:39] tail -n +1 /app/public/converted_csv/hungary_sp_list_nodes_16124.csv >> /app/public/diff/hungary_sp_list_nodes_16124.diff
[CMD] [2019-10-13 11:17:39] echo "." >> /app/public/diff/hungary_sp_list_nodes_16124.diff
[CMD] [2019-10-13 11:17:39] echo "0a" > /app/public/diff/hungary_sp_list_occurrences_16125.diff
[CMD] [2019-10-13 11:17:39] tail -n +1 /app/public/converted_csv/hungary_sp_list_occurrences_16125.csv >> /app/public/diff/hungary_sp_list_occurrences_16125.diff
[CMD] [2019-10-13 11:17:39] echo "." >> /app/public/diff/hungary_sp_list_occurrences_16125.diff
[CMD] [2019-10-13 11:17:39] echo "0a" > /app/public/diff/hungary_sp_list_measurements_16126.diff
[CMD] [2019-10-13 11:17:39] tail -n +1 /app/public/converted_csv/hungary_sp_list_measurements_16126.csv >> /app/public/diff/hungary_sp_list_measurements_16126.diff
[CMD] [2019-10-13 11:17:39] echo "." >> /app/public/diff/hungary_sp_list_measurements_16126.diff
[STOP] [2019-10-13 11:17:39] calculate_delta
[START] [2019-10-13 11:17:39] parse_diff_and_store
[INFO] [2019-10-13 11:17:39] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 11:17:40] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 11:17:45] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 11:17:46] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 11:18:31] Storing 2 References
[INFO] [2019-10-13 11:18:31] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 11:18:31] Average Time: 0.0
[INFO] [2019-10-13 11:18:31] Total Time: 1s
[INFO] [2019-10-13 11:18:31] Storing 13165 ScientificNames
[INFO] [2019-10-13 11:18:31] Processing group of 13165 in 14 groups of 1000
[INFO] [2019-10-13 11:18:36] Average Time: 0.339
[INFO] [2019-10-13 11:18:36] Total Time: 5s
[INFO] [2019-10-13 11:18:36] last 3 / first 3: 0.68
[INFO] [2019-10-13 11:18:36] Std.Dev: 0.08366600265340755; Max: 0.39
[INFO] [2019-10-13 11:18:36] Storing 13165 Nodes
[INFO] [2019-10-13 11:18:36] Processing group of 13165 in 14 groups of 1000
[INFO] [2019-10-13 11:18:40] Average Time: 0.314
[INFO] [2019-10-13 11:18:40] Total Time: 5s
[INFO] [2019-10-13 11:18:40] last 3 / first 3: 0.54
[INFO] [2019-10-13 11:18:40] Std.Dev: 0.1224744871391589; Max: 0.62
[INFO] [2019-10-13 11:18:40] Storing 7712 Occurrences
[INFO] [2019-10-13 11:18:40] Processing group of 7712 in 8 groups of 1000
[INFO] [2019-10-13 11:18:41] Average Time: 0.096
[INFO] [2019-10-13 11:18:41] Total Time: 1s
[INFO] [2019-10-13 11:18:41] last 3 / first 3: 0.87
[INFO] [2019-10-13 11:18:41] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-13 11:18:41] Storing 15672 TraitsReferences
[INFO] [2019-10-13 11:18:41] Processing group of 15672 in 16 groups of 1000
[INFO] [2019-10-13 11:18:42] Average Time: 0.074
[INFO] [2019-10-13 11:18:42] Total Time: 2s
[INFO] [2019-10-13 11:18:42] last 3 / first 3: 0.64
[INFO] [2019-10-13 11:18:42] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-13 11:18:42] Storing 15671 Traits
[INFO] [2019-10-13 11:18:42] Processing group of 15671 in 16 groups of 1000
[INFO] [2019-10-13 11:18:47] Average Time: 0.311
[INFO] [2019-10-13 11:18:47] Total Time: 6s
[INFO] [2019-10-13 11:18:47] last 3 / first 3: 0.76
[INFO] [2019-10-13 11:18:47] Std.Dev: 0.044721359549995794; Max: 0.41
[INFO] [2019-10-13 11:18:47] Storing 15658 MetaTraits
[INFO] [2019-10-13 11:18:47] Processing group of 15658 in 16 groups of 1000
[INFO] [2019-10-13 11:18:50] Average Time: 0.143
[INFO] [2019-10-13 11:18:50] Total Time: 3s
[INFO] [2019-10-13 11:18:50] last 3 / first 3: 1.04
[INFO] [2019-10-13 11:18:50] Std.Dev: 0.0; Max: 0.17
[STOP] [2019-10-13 11:18:50] parse_diff_and_store
[START] [2019-10-13 11:18:50] resolve_keys
[INFO] [2019-10-13 11:19:38] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 11:19:42] traits to occurrences...
[INFO] [2019-10-13 11:19:48] traits to nodes (through occurrences)...
[INFO] [2019-10-13 11:19:49] Traits to sex term...
[INFO] [2019-10-13 11:19:53] Traits to lifestage term...
[INFO] [2019-10-13 11:19:58] MetaTraits to traits...
[INFO] [2019-10-13 11:19:59] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 11:20:02] Assocs to occurrences...
[INFO] [2019-10-13 11:20:02] Assocs to nodes...
[INFO] [2019-10-13 11:20:02] Assoc to sex term...
[INFO] [2019-10-13 11:20:02] Assoc to lifestage term...
[STOP] [2019-10-13 11:20:02] resolve_keys
[START] [2019-10-13 11:20:02] hold_for_later_1
[STOP] [2019-10-13 11:20:02] hold_for_later_1
[START] [2019-10-13 11:20:02] hold_for_later_2
[STOP] [2019-10-13 11:20:02] hold_for_later_2
[START] [2019-10-13 11:20:02] resolve_missing_parents
[STOP] [2019-10-13 11:20:26] resolve_missing_parents
[START] [2019-10-13 11:20:26] rebuild_nodes
[START] [2019-10-13 11:20:26] Flattener#flatten
[START] [2019-10-13 11:20:26] Flattener#study_resource
[START] [2019-10-13 11:20:26] Flattener#build_ancestry
[STOP] [2019-10-13 11:20:26] Flattener#build_ancestry
[INFO] [2019-10-13 11:20:26] 13165 ancestry keys
[START] [2019-10-13 11:20:26] build_node_ancestors
[INFO] [2019-10-13 11:20:26] old ancestors deleted.
[STOP] [2019-10-13 11:20:30] build_node_ancestors
[START] [2019-10-13 11:20:33] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 11:20:34] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 11:20:34] Flattener#flatten
[STOP] [2019-10-13 11:20:34] rebuild_nodes
[START] [2019-10-13 11:20:34] resolve_missing_media_owners
[STOP] [2019-10-13 11:20:34] resolve_missing_media_owners
[START] [2019-10-13 11:20:34] sanitize_media_verbatims
[STOP] [2019-10-13 11:20:34] sanitize_media_verbatims
[START] [2019-10-13 11:20:34] queue_downloads
[STOP] [2019-10-13 11:20:34] queue_downloads
[START] [2019-10-13 11:20:34] parse_names
[WARN] [2019-10-13 11:20:34] I see 13165 names which still need to be parsed.
[STOP] [2019-10-13 11:20:45] parse_names
[START] [2019-10-13 11:20:45] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 11:20:45] denormalize_canonical_names_to_nodes
[START] [2019-10-13 11:20:45] match_nodes
[START] [2019-10-13 11:20:45] map_all_nodes_to_pages
[STOP] [2019-10-13 11:35:20] map_all_nodes_to_pages
[INFO] [2019-10-13 11:35:20] 1705 Unmatched nodes (of 13165)! That's too many to output. First 10: Magnoliopsida (#50080081); Cytisus pannonicus (#50082622); Melilotus alba (#50086529); Ranunculus calthifolia (#50093234); Anemone vulgaris (#50084145); Anemone narcissiflorum (#50088021); Delphinium cultorum (#50090615); Delphinium hybridum (#50092038); Thalictrum glandulosum (#50091236); Artemisia maritima (#50088378)
[START] [2019-10-13 11:35:20] update_nodes
[STOP] [2019-10-13 11:35:24] update_nodes
[STOP] [2019-10-13 11:35:24] match_nodes
[START] [2019-10-13 11:35:24] reindex_search
[STOP] [2019-10-13 11:36:01] reindex_search
[START] [2019-10-13 11:36:01] normalize_units
[STOP] [2019-10-13 11:36:01] normalize_units
[START] [2019-10-13 11:36:01] calculate_statistics
[STOP] [2019-10-13 11:36:01] calculate_statistics
[START] [2019-10-13 11:36:01] complete_harvest_instance
[START] [2019-10-13 11:36:01] overall_tsv_creation
[INFO] [2019-10-13 11:36:01] Processing group of 13165 in 2 batches of 10000
[INFO] [2019-10-13 11:37:30] 5726 Traits (unfiltered)...
[INFO] [2019-10-13 11:37:45] 5726 Traits (filtered)...
[INFO] [2019-10-13 11:37:45] 0 Associations (filtered)...
[INFO] [2019-10-13 11:38:35] 28622 metadata added.
[INFO] [2019-10-13 11:38:35] 0 metadata added.
[INFO] [2019-10-13 11:39:35] 1986 Traits (unfiltered)...
[INFO] [2019-10-13 11:39:49] 1986 Traits (filtered)...
[INFO] [2019-10-13 11:39:49] 0 Associations (filtered)...
[INFO] [2019-10-13 11:40:30] 9925 metadata added.
[INFO] [2019-10-13 11:40:30] 0 metadata added.
[INFO] [2019-10-13 11:40:30] Average Time: 110.04
[INFO] [2019-10-13 11:40:30] Total Time: 4m30s
[STOP] [2019-10-13 11:40:30] overall_tsv_creation
[INFO] [2019-10-13 11:40:30] Done. Check your files:
[INFO] [2019-10-13 11:40:30] (13165 lines) /app/public/data/hungary_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 11:40:30] (43959 lines) /app/public/data/hungary_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 11:40:30] (13165 lines) /app/public/data/hungary_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 11:40:30] (7713 lines) /app/public/data/hungary_sp_list/publish_traits.tsv
[INFO] [2019-10-13 11:40:30] (38548 lines) /app/public/data/hungary_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 11:40:31] complete_harvest_instance
[START] [2019-10-13 11:40:31] completed
[STOP] [2019-10-13 11:40:31] completed
[STOP] [2019-10-13 11:40:31] logged process, took 1375.19

Latest Process