Harvest for Madagascar Species List Created 14 Oct 03:02

Stage: completed
Fetched: 14 Oct 03:02
Validated: 14 Oct 03:02
Deltas Created 14 Oct 03:02
Units Normalized: 14 Oct 03:30
Ancestry Built: 14 Oct 03:08
Nodes Matched: 14 Oct 03:29
Names Parsed: 14 Oct 03:08
New Models Stored: 14 Oct 03:05
Indexed: 14 Oct 03:30
Completed: 14 Oct 03:37
Time to Harvest: 1 minute
Harvesting Log

(161 lines)
# Logfile created on 2019-10-14 03:02:21 -0400 by logger.rb/56815
[START] [2019-10-14 03:02:21] logged process
[START] [2019-10-14 03:02:21] create_harvest_instance
[STOP] [2019-10-14 03:02:22] create_harvest_instance
[START] [2019-10-14 03:02:22] fetch_files
[STOP] [2019-10-14 03:02:22] fetch_files
[START] [2019-10-14 03:02:22] validate_each_file
[STOP] [2019-10-14 03:02:25] validate_each_file
[START] [2019-10-14 03:02:25] convert_to_csv
[CMD] [2019-10-14 03:02:25] /usr/bin/sort /app/public/converted_csv/madagascar_sp_li_refs_16467.csv > /app/public/converted_csv/madagascar_sp_li_refs_16467.csv_sorted
[CMD] [2019-10-14 03:02:25] /usr/bin/sort /app/public/converted_csv/madagascar_sp_li_nodes_16468.csv > /app/public/converted_csv/madagascar_sp_li_nodes_16468.csv_sorted
[CMD] [2019-10-14 03:02:26] /usr/bin/sort /app/public/converted_csv/madagascar_sp_li_occurrences_16469.csv > /app/public/converted_csv/madagascar_sp_li_occurrences_16469.csv_sorted
[CMD] [2019-10-14 03:02:26] /usr/bin/sort /app/public/converted_csv/madagascar_sp_li_measurements_16470.csv > /app/public/converted_csv/madagascar_sp_li_measurements_16470.csv_sorted
[STOP] [2019-10-14 03:02:26] convert_to_csv
[START] [2019-10-14 03:02:26] calculate_delta
[CMD] [2019-10-14 03:02:26] echo "0a" > /app/public/diff/madagascar_sp_li_refs_16467.diff
[CMD] [2019-10-14 03:02:26] tail -n +1 /app/public/converted_csv/madagascar_sp_li_refs_16467.csv >> /app/public/diff/madagascar_sp_li_refs_16467.diff
[CMD] [2019-10-14 03:02:26] echo "." >> /app/public/diff/madagascar_sp_li_refs_16467.diff
[CMD] [2019-10-14 03:02:26] echo "0a" > /app/public/diff/madagascar_sp_li_nodes_16468.diff
[CMD] [2019-10-14 03:02:26] tail -n +1 /app/public/converted_csv/madagascar_sp_li_nodes_16468.csv >> /app/public/diff/madagascar_sp_li_nodes_16468.diff
[CMD] [2019-10-14 03:02:26] echo "." >> /app/public/diff/madagascar_sp_li_nodes_16468.diff
[CMD] [2019-10-14 03:02:26] echo "0a" > /app/public/diff/madagascar_sp_li_occurrences_16469.diff
[CMD] [2019-10-14 03:02:26] tail -n +1 /app/public/converted_csv/madagascar_sp_li_occurrences_16469.csv >> /app/public/diff/madagascar_sp_li_occurrences_16469.diff
[CMD] [2019-10-14 03:02:27] echo "." >> /app/public/diff/madagascar_sp_li_occurrences_16469.diff
[CMD] [2019-10-14 03:02:27] echo "0a" > /app/public/diff/madagascar_sp_li_measurements_16470.diff
[CMD] [2019-10-14 03:02:27] tail -n +1 /app/public/converted_csv/madagascar_sp_li_measurements_16470.csv >> /app/public/diff/madagascar_sp_li_measurements_16470.diff
[CMD] [2019-10-14 03:02:27] echo "." >> /app/public/diff/madagascar_sp_li_measurements_16470.diff
[STOP] [2019-10-14 03:02:27] calculate_delta
[START] [2019-10-14 03:02:27] parse_diff_and_store
[INFO] [2019-10-14 03:02:27] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 03:02:27] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 03:02:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 03:02:40] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 03:04:35] Storing 2 References
[INFO] [2019-10-14 03:04:35] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 03:04:35] Average Time: 0.0
[INFO] [2019-10-14 03:04:35] Total Time: 1s
[INFO] [2019-10-14 03:04:35] Storing 25941 ScientificNames
[INFO] [2019-10-14 03:04:35] Processing group of 25941 in 26 groups of 1000
[INFO] [2019-10-14 03:04:44] Average Time: 0.365
[INFO] [2019-10-14 03:04:44] Total Time: 10s
[INFO] [2019-10-14 03:04:44] last 3 / first 3: 0.96
[INFO] [2019-10-14 03:04:44] Std.Dev: 0.03162277660168379; Max: 0.44
[INFO] [2019-10-14 03:04:44] Storing 25941 Nodes
[INFO] [2019-10-14 03:04:44] Processing group of 25941 in 26 groups of 1000
[INFO] [2019-10-14 03:04:53] Average Time: 0.338
[INFO] [2019-10-14 03:04:53] Total Time: 9s
[INFO] [2019-10-14 03:04:53] last 3 / first 3: 0.51
[INFO] [2019-10-14 03:04:53] Std.Dev: 0.1341640786499874; Max: 0.84
[INFO] [2019-10-14 03:04:53] Storing 19762 Occurrences
[INFO] [2019-10-14 03:04:53] Processing group of 19762 in 20 groups of 1000
[INFO] [2019-10-14 03:04:55] Average Time: 0.101
[INFO] [2019-10-14 03:04:55] Total Time: 3s
[INFO] [2019-10-14 03:04:55] last 3 / first 3: 1.0
[INFO] [2019-10-14 03:04:55] Std.Dev: 0.0; Max: 0.12
[INFO] [2019-10-14 03:04:55] Storing 39730 TraitsReferences
[INFO] [2019-10-14 03:04:55] Processing group of 39730 in 40 groups of 1000
[INFO] [2019-10-14 03:04:58] Average Time: 0.073
[INFO] [2019-10-14 03:04:58] Total Time: 4s
[INFO] [2019-10-14 03:04:58] last 3 / first 3: 0.68
[INFO] [2019-10-14 03:04:58] Std.Dev: 0.0; Max: 0.16
[INFO] [2019-10-14 03:04:58] Storing 39729 Traits
[INFO] [2019-10-14 03:04:58] Processing group of 39729 in 40 groups of 1000
[INFO] [2019-10-14 03:05:12] Average Time: 0.33
[INFO] [2019-10-14 03:05:12] Total Time: 14s
[INFO] [2019-10-14 03:05:12] last 3 / first 3: 0.75
[INFO] [2019-10-14 03:05:12] Std.Dev: 0.10954451150103323; Max: 0.85
[INFO] [2019-10-14 03:05:12] Storing 39701 MetaTraits
[INFO] [2019-10-14 03:05:12] Processing group of 39701 in 40 groups of 1000
[INFO] [2019-10-14 03:05:18] Average Time: 0.148
[INFO] [2019-10-14 03:05:18] Total Time: 7s
[INFO] [2019-10-14 03:05:18] last 3 / first 3: 0.95
[INFO] [2019-10-14 03:05:18] Std.Dev: 0.08366600265340755; Max: 0.56
[STOP] [2019-10-14 03:05:18] parse_diff_and_store
[START] [2019-10-14 03:05:18] resolve_keys
[INFO] [2019-10-14 03:06:44] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 03:06:51] traits to occurrences...
[INFO] [2019-10-14 03:06:56] traits to nodes (through occurrences)...
[INFO] [2019-10-14 03:06:57] Traits to sex term...
[INFO] [2019-10-14 03:07:02] Traits to lifestage term...
[INFO] [2019-10-14 03:07:08] MetaTraits to traits...
[INFO] [2019-10-14 03:07:10] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 03:07:16] Assocs to occurrences...
[INFO] [2019-10-14 03:07:16] Assocs to nodes...
[INFO] [2019-10-14 03:07:16] Assoc to sex term...
[INFO] [2019-10-14 03:07:16] Assoc to lifestage term...
[STOP] [2019-10-14 03:07:16] resolve_keys
[START] [2019-10-14 03:07:16] hold_for_later_1
[STOP] [2019-10-14 03:07:16] hold_for_later_1
[START] [2019-10-14 03:07:16] hold_for_later_2
[STOP] [2019-10-14 03:07:16] hold_for_later_2
[START] [2019-10-14 03:07:16] resolve_missing_parents
[STOP] [2019-10-14 03:08:06] resolve_missing_parents
[START] [2019-10-14 03:08:06] rebuild_nodes
[START] [2019-10-14 03:08:06] Flattener#flatten
[START] [2019-10-14 03:08:06] Flattener#study_resource
[START] [2019-10-14 03:08:06] Flattener#build_ancestry
[STOP] [2019-10-14 03:08:08] Flattener#build_ancestry
[INFO] [2019-10-14 03:08:08] 25941 ancestry keys
[START] [2019-10-14 03:08:08] build_node_ancestors
[INFO] [2019-10-14 03:08:08] old ancestors deleted.
[STOP] [2019-10-14 03:08:13] build_node_ancestors
[START] [2019-10-14 03:08:17] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 03:08:19] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 03:08:19] Flattener#flatten
[STOP] [2019-10-14 03:08:19] rebuild_nodes
[START] [2019-10-14 03:08:19] resolve_missing_media_owners
[STOP] [2019-10-14 03:08:19] resolve_missing_media_owners
[START] [2019-10-14 03:08:19] sanitize_media_verbatims
[STOP] [2019-10-14 03:08:19] sanitize_media_verbatims
[START] [2019-10-14 03:08:19] queue_downloads
[STOP] [2019-10-14 03:08:19] queue_downloads
[START] [2019-10-14 03:08:19] parse_names
[WARN] [2019-10-14 03:08:19] I see 25941 names which still need to be parsed.
[STOP] [2019-10-14 03:08:41] parse_names
[START] [2019-10-14 03:08:41] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 03:08:41] denormalize_canonical_names_to_nodes
[START] [2019-10-14 03:08:41] match_nodes
[START] [2019-10-14 03:08:41] map_all_nodes_to_pages
[STOP] [2019-10-14 03:28:56] map_all_nodes_to_pages
[INFO] [2019-10-14 03:28:56] 1645 Unmatched nodes (of 25941)! That's too many to output. First 10: Monomorium micrommaton (#50580272); Monomorium nigricans (#50580536); Monomorium fisheri (#50580542); Monomorium chnodes (#50580555); Monomorium versicolor (#50580646); Monomorium lepidum (#50581098); Monomorium flavimembra (#50581191); Monomorium platynodis (#50582640); Monomorium xuthosoma (#50582990); Monomorium bifidoclypeatum (#50583004)
[START] [2019-10-14 03:28:56] update_nodes
[STOP] [2019-10-14 03:29:05] update_nodes
[STOP] [2019-10-14 03:29:05] match_nodes
[START] [2019-10-14 03:29:05] reindex_search
[STOP] [2019-10-14 03:30:02] reindex_search
[START] [2019-10-14 03:30:02] normalize_units
[STOP] [2019-10-14 03:30:02] normalize_units
[START] [2019-10-14 03:30:02] calculate_statistics
[STOP] [2019-10-14 03:30:02] calculate_statistics
[START] [2019-10-14 03:30:02] complete_harvest_instance
[START] [2019-10-14 03:30:02] overall_tsv_creation
[INFO] [2019-10-14 03:30:02] Processing group of 25941 in 3 batches of 10000
[INFO] [2019-10-14 03:31:31] 7259 Traits (unfiltered)...
[INFO] [2019-10-14 03:31:44] 7259 Traits (filtered)...
[INFO] [2019-10-14 03:31:45] 0 Associations (filtered)...
[INFO] [2019-10-14 03:32:36] 36288 metadata added.
[INFO] [2019-10-14 03:32:36] 0 metadata added.
[INFO] [2019-10-14 03:34:09] 7920 Traits (unfiltered)...
[INFO] [2019-10-14 03:34:23] 7920 Traits (filtered)...
[INFO] [2019-10-14 03:34:23] 0 Associations (filtered)...
[INFO] [2019-10-14 03:35:18] 39589 metadata added.
[INFO] [2019-10-14 03:35:18] 0 metadata added.
[INFO] [2019-10-14 03:36:32] 4583 Traits (unfiltered)...
[INFO] [2019-10-14 03:36:46] 4583 Traits (filtered)...
[INFO] [2019-10-14 03:36:46] 0 Associations (filtered)...
[INFO] [2019-10-14 03:37:33] 22904 metadata added.
[INFO] [2019-10-14 03:37:33] 0 metadata added.
[INFO] [2019-10-14 03:37:33] Average Time: 124.577
[INFO] [2019-10-14 03:37:33] Total Time: 7m32s
[STOP] [2019-10-14 03:37:33] overall_tsv_creation
[INFO] [2019-10-14 03:37:33] Done. Check your files:
[INFO] [2019-10-14 03:37:33] (25941 lines) /app/public/data/madagascar_sp_li/publish_nodes.tsv
[INFO] [2019-10-14 03:37:33] (68628 lines) /app/public/data/madagascar_sp_li/publish_node_ancestors.tsv
[INFO] [2019-10-14 03:37:33] (25941 lines) /app/public/data/madagascar_sp_li/publish_scientific_names.tsv
[INFO] [2019-10-14 03:37:34] (19763 lines) /app/public/data/madagascar_sp_li/publish_traits.tsv
[INFO] [2019-10-14 03:37:34] (98782 lines) /app/public/data/madagascar_sp_li/publish_metadata.tsv
[STOP] [2019-10-14 03:37:34] complete_harvest_instance
[START] [2019-10-14 03:37:34] completed
[STOP] [2019-10-14 03:37:34] completed
[STOP] [2019-10-14 03:37:34] logged process, took 2112.57
Latest Process

14 Oct 03:02 EXITED currently processing 0