Harvest for Malawi Species List Created 14 Oct 04:00

Stage: completed
Fetched: 14 Oct 04:00
Validated: 14 Oct 04:00
Deltas Created 14 Oct 04:00
Units Normalized: 14 Oct 04:08
Ancestry Built: 14 Oct 04:02
Nodes Matched: 14 Oct 04:08
Names Parsed: 14 Oct 04:02
New Models Stored: 14 Oct 04:00
Indexed: 14 Oct 04:08
Completed: 14 Oct 04:10
Time to Harvest: less than a minute
Harvesting Log

(149 lines)
# Logfile created on 2019-10-14 04:00:10 -0400 by logger.rb/56815
[START] [2019-10-14 04:00:10] logged process
[START] [2019-10-14 04:00:10] create_harvest_instance
[STOP] [2019-10-14 04:00:10] create_harvest_instance
[START] [2019-10-14 04:00:10] fetch_files
[STOP] [2019-10-14 04:00:10] fetch_files
[START] [2019-10-14 04:00:10] validate_each_file
[STOP] [2019-10-14 04:00:11] validate_each_file
[START] [2019-10-14 04:00:11] convert_to_csv
[CMD] [2019-10-14 04:00:11] /usr/bin/sort /app/public/converted_csv/malawi_sp_list_refs_16491.csv > /app/public/converted_csv/malawi_sp_list_refs_16491.csv_sorted
[CMD] [2019-10-14 04:00:11] /usr/bin/sort /app/public/converted_csv/malawi_sp_list_nodes_16492.csv > /app/public/converted_csv/malawi_sp_list_nodes_16492.csv_sorted
[CMD] [2019-10-14 04:00:11] /usr/bin/sort /app/public/converted_csv/malawi_sp_list_occurrences_16493.csv > /app/public/converted_csv/malawi_sp_list_occurrences_16493.csv_sorted
[CMD] [2019-10-14 04:00:11] /usr/bin/sort /app/public/converted_csv/malawi_sp_list_measurements_16494.csv > /app/public/converted_csv/malawi_sp_list_measurements_16494.csv_sorted
[STOP] [2019-10-14 04:00:12] convert_to_csv
[START] [2019-10-14 04:00:12] calculate_delta
[CMD] [2019-10-14 04:00:12] echo "0a" > /app/public/diff/malawi_sp_list_refs_16491.diff
[CMD] [2019-10-14 04:00:12] tail -n +1 /app/public/converted_csv/malawi_sp_list_refs_16491.csv >> /app/public/diff/malawi_sp_list_refs_16491.diff
[CMD] [2019-10-14 04:00:12] echo "." >> /app/public/diff/malawi_sp_list_refs_16491.diff
[CMD] [2019-10-14 04:00:12] echo "0a" > /app/public/diff/malawi_sp_list_nodes_16492.diff
[CMD] [2019-10-14 04:00:12] tail -n +1 /app/public/converted_csv/malawi_sp_list_nodes_16492.csv >> /app/public/diff/malawi_sp_list_nodes_16492.diff
[CMD] [2019-10-14 04:00:12] echo "." >> /app/public/diff/malawi_sp_list_nodes_16492.diff
[CMD] [2019-10-14 04:00:12] echo "0a" > /app/public/diff/malawi_sp_list_occurrences_16493.diff
[CMD] [2019-10-14 04:00:12] tail -n +1 /app/public/converted_csv/malawi_sp_list_occurrences_16493.csv >> /app/public/diff/malawi_sp_list_occurrences_16493.diff
[CMD] [2019-10-14 04:00:12] echo "." >> /app/public/diff/malawi_sp_list_occurrences_16493.diff
[CMD] [2019-10-14 04:00:12] echo "0a" > /app/public/diff/malawi_sp_list_measurements_16494.diff
[CMD] [2019-10-14 04:00:13] tail -n +1 /app/public/converted_csv/malawi_sp_list_measurements_16494.csv >> /app/public/diff/malawi_sp_list_measurements_16494.diff
[CMD] [2019-10-14 04:00:13] echo "." >> /app/public/diff/malawi_sp_list_measurements_16494.diff
[STOP] [2019-10-14 04:00:13] calculate_delta
[START] [2019-10-14 04:00:13] parse_diff_and_store
[INFO] [2019-10-14 04:00:13] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-14 04:00:13] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-14 04:00:16] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-14 04:00:17] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-14 04:00:45] Storing 2 References
[INFO] [2019-10-14 04:00:45] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-14 04:00:45] Average Time: 0.0
[INFO] [2019-10-14 04:00:45] Total Time: 1s
[INFO] [2019-10-14 04:00:45] Storing 7389 ScientificNames
[INFO] [2019-10-14 04:00:45] Processing group of 7389 in 8 groups of 1000
[INFO] [2019-10-14 04:00:48] Average Time: 0.357
[INFO] [2019-10-14 04:00:48] Total Time: 3s
[INFO] [2019-10-14 04:00:48] last 3 / first 3: 0.81
[INFO] [2019-10-14 04:00:48] Std.Dev: 0.06324555320336758; Max: 0.45
[INFO] [2019-10-14 04:00:48] Storing 7389 Nodes
[INFO] [2019-10-14 04:00:48] Processing group of 7389 in 8 groups of 1000
[INFO] [2019-10-14 04:00:50] Average Time: 0.281
[INFO] [2019-10-14 04:00:50] Total Time: 3s
[INFO] [2019-10-14 04:00:50] last 3 / first 3: 0.74
[INFO] [2019-10-14 04:00:50] Std.Dev: 0.06324555320336758; Max: 0.33
[INFO] [2019-10-14 04:00:50] Storing 4820 Occurrences
[INFO] [2019-10-14 04:00:50] Processing group of 4820 in 5 groups of 1000
[INFO] [2019-10-14 04:00:51] Average Time: 0.096
[INFO] [2019-10-14 04:00:51] Total Time: 1s
[INFO] [2019-10-14 04:00:51] Storing 9790 TraitsReferences
[INFO] [2019-10-14 04:00:51] Processing group of 9790 in 10 groups of 1000
[INFO] [2019-10-14 04:00:52] Average Time: 0.086
[INFO] [2019-10-14 04:00:52] Total Time: 1s
[INFO] [2019-10-14 04:00:52] last 3 / first 3: 0.65
[INFO] [2019-10-14 04:00:52] Std.Dev: 0.03162277660168379; Max: 0.15
[INFO] [2019-10-14 04:00:52] Storing 9789 Traits
[INFO] [2019-10-14 04:00:52] Processing group of 9789 in 10 groups of 1000
[INFO] [2019-10-14 04:00:55] Average Time: 0.302
[INFO] [2019-10-14 04:00:55] Total Time: 4s
[INFO] [2019-10-14 04:00:55] last 3 / first 3: 0.79
[INFO] [2019-10-14 04:00:55] Std.Dev: 0.05477225575051661; Max: 0.44
[INFO] [2019-10-14 04:00:55] Storing 9789 MetaTraits
[INFO] [2019-10-14 04:00:55] Processing group of 9789 in 10 groups of 1000
[INFO] [2019-10-14 04:00:56] Average Time: 0.122
[INFO] [2019-10-14 04:00:56] Total Time: 2s
[INFO] [2019-10-14 04:00:56] last 3 / first 3: 0.68
[INFO] [2019-10-14 04:00:56] Std.Dev: 0.03162277660168379; Max: 0.18
[STOP] [2019-10-14 04:00:56] parse_diff_and_store
[START] [2019-10-14 04:00:56] resolve_keys
[INFO] [2019-10-14 04:01:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-14 04:01:33] traits to occurrences...
[INFO] [2019-10-14 04:01:35] traits to nodes (through occurrences)...
[INFO] [2019-10-14 04:01:35] Traits to sex term...
[INFO] [2019-10-14 04:01:37] Traits to lifestage term...
[INFO] [2019-10-14 04:01:38] MetaTraits to traits...
[INFO] [2019-10-14 04:01:39] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-14 04:01:40] Assocs to occurrences...
[INFO] [2019-10-14 04:01:40] Assocs to nodes...
[INFO] [2019-10-14 04:01:40] Assoc to sex term...
[INFO] [2019-10-14 04:01:40] Assoc to lifestage term...
[STOP] [2019-10-14 04:01:40] resolve_keys
[START] [2019-10-14 04:01:40] hold_for_later_1
[STOP] [2019-10-14 04:01:40] hold_for_later_1
[START] [2019-10-14 04:01:40] hold_for_later_2
[STOP] [2019-10-14 04:01:40] hold_for_later_2
[START] [2019-10-14 04:01:40] resolve_missing_parents
[STOP] [2019-10-14 04:01:58] resolve_missing_parents
[START] [2019-10-14 04:01:58] rebuild_nodes
[START] [2019-10-14 04:01:58] Flattener#flatten
[START] [2019-10-14 04:01:58] Flattener#study_resource
[START] [2019-10-14 04:01:58] Flattener#build_ancestry
[STOP] [2019-10-14 04:01:58] Flattener#build_ancestry
[INFO] [2019-10-14 04:01:58] 7389 ancestry keys
[START] [2019-10-14 04:01:58] build_node_ancestors
[INFO] [2019-10-14 04:01:58] old ancestors deleted.
[STOP] [2019-10-14 04:02:00] build_node_ancestors
[START] [2019-10-14 04:02:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 04:02:01] Flattener#propagate_ancestor_ids
[STOP] [2019-10-14 04:02:01] Flattener#flatten
[STOP] [2019-10-14 04:02:01] rebuild_nodes
[START] [2019-10-14 04:02:01] resolve_missing_media_owners
[STOP] [2019-10-14 04:02:01] resolve_missing_media_owners
[START] [2019-10-14 04:02:01] sanitize_media_verbatims
[STOP] [2019-10-14 04:02:01] sanitize_media_verbatims
[START] [2019-10-14 04:02:01] queue_downloads
[STOP] [2019-10-14 04:02:01] queue_downloads
[START] [2019-10-14 04:02:01] parse_names
[WARN] [2019-10-14 04:02:01] I see 7389 names which still need to be parsed.
[STOP] [2019-10-14 04:02:10] parse_names
[START] [2019-10-14 04:02:10] denormalize_canonical_names_to_nodes
[STOP] [2019-10-14 04:02:10] denormalize_canonical_names_to_nodes
[START] [2019-10-14 04:02:10] match_nodes
[START] [2019-10-14 04:02:10] map_all_nodes_to_pages
[STOP] [2019-10-14 04:08:15] map_all_nodes_to_pages
[INFO] [2019-10-14 04:08:15] 387 Unmatched nodes (of 7389)! That's too many to output. First 10: Andropadus virens (#50614698); Andropadus milanjensis (#50615058); Andropadus tephrolaemus (#50615179); Andropadus masukuensis (#50620485); Arizelocichla tephrolaemus (#50614911); Euplectes macrourus (#50614768); Spermestes bicolor (#50614640); Spermestes cucullatus (#50614645); Spermestes fringilloides (#50615709); Sylvia abyssinica (#50620383)
[START] [2019-10-14 04:08:15] update_nodes
[STOP] [2019-10-14 04:08:17] update_nodes
[STOP] [2019-10-14 04:08:17] match_nodes
[START] [2019-10-14 04:08:17] reindex_search
[STOP] [2019-10-14 04:08:33] reindex_search
[START] [2019-10-14 04:08:33] normalize_units
[STOP] [2019-10-14 04:08:33] normalize_units
[START] [2019-10-14 04:08:33] calculate_statistics
[STOP] [2019-10-14 04:08:33] calculate_statistics
[START] [2019-10-14 04:08:33] complete_harvest_instance
[START] [2019-10-14 04:08:33] overall_tsv_creation
[INFO] [2019-10-14 04:08:33] Processing group of 7389 in 1 batches of 10000
[INFO] [2019-10-14 04:09:54] 4820 Traits (unfiltered)...
[INFO] [2019-10-14 04:10:08] 4820 Traits (filtered)...
[INFO] [2019-10-14 04:10:08] 0 Associations (filtered)...
[INFO] [2019-10-14 04:10:56] 24099 metadata added.
[INFO] [2019-10-14 04:10:56] 0 metadata added.
[INFO] [2019-10-14 04:10:56] Average Time: 114.8
[INFO] [2019-10-14 04:10:56] Total Time: 2m23s
[STOP] [2019-10-14 04:10:56] overall_tsv_creation
[INFO] [2019-10-14 04:10:56] Done. Check your files:
[INFO] [2019-10-14 04:10:56] (7389 lines) /app/public/data/malawi_sp_list/publish_nodes.tsv
[INFO] [2019-10-14 04:10:56] (16315 lines) /app/public/data/malawi_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-14 04:10:56] (7389 lines) /app/public/data/malawi_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-14 04:10:56] (4821 lines) /app/public/data/malawi_sp_list/publish_traits.tsv
[INFO] [2019-10-14 04:10:56] (24100 lines) /app/public/data/malawi_sp_list/publish_metadata.tsv
[STOP] [2019-10-14 04:10:56] complete_harvest_instance
[START] [2019-10-14 04:10:56] completed
[STOP] [2019-10-14 04:10:56] completed
[STOP] [2019-10-14 04:10:56] logged process, took 646.81
Latest Process

14 Oct 04:00 EXITED currently processing 0