Harvest for Jamaica Species List Created 13 Oct 21:17

Stage: completed
Fetched: 13 Oct 21:17
Validated: 13 Oct 21:17
Deltas Created 13 Oct 21:18
Units Normalized: 13 Oct 21:30
Ancestry Built: 13 Oct 21:20
Nodes Matched: 13 Oct 21:29
Names Parsed: 13 Oct 21:20
New Models Stored: 13 Oct 21:18
Indexed: 13 Oct 21:30
Completed: 13 Oct 21:34
Time to Harvest: less than a minute
Harvesting Log

(156 lines)
# Logfile created on 2019-10-13 21:17:55 -0400 by logger.rb/56815
[START] [2019-10-13 21:17:55] logged process
[START] [2019-10-13 21:17:55] create_harvest_instance
[STOP] [2019-10-13 21:17:56] create_harvest_instance
[START] [2019-10-13 21:17:56] fetch_files
[STOP] [2019-10-13 21:17:56] fetch_files
[START] [2019-10-13 21:17:56] validate_each_file
[STOP] [2019-10-13 21:17:58] validate_each_file
[START] [2019-10-13 21:17:58] convert_to_csv
[CMD] [2019-10-13 21:17:58] /usr/bin/sort /app/public/converted_csv/jamaica_sp_list_refs_16243.csv > /app/public/converted_csv/jamaica_sp_list_refs_16243.csv_sorted
[CMD] [2019-10-13 21:17:58] /usr/bin/sort /app/public/converted_csv/jamaica_sp_list_nodes_16244.csv > /app/public/converted_csv/jamaica_sp_list_nodes_16244.csv_sorted
[CMD] [2019-10-13 21:17:59] /usr/bin/sort /app/public/converted_csv/jamaica_sp_list_occurrences_16245.csv > /app/public/converted_csv/jamaica_sp_list_occurrences_16245.csv_sorted
[CMD] [2019-10-13 21:17:59] /usr/bin/sort /app/public/converted_csv/jamaica_sp_list_measurements_16246.csv > /app/public/converted_csv/jamaica_sp_list_measurements_16246.csv_sorted
[STOP] [2019-10-13 21:17:59] convert_to_csv
[START] [2019-10-13 21:17:59] calculate_delta
[CMD] [2019-10-13 21:17:59] echo "0a" > /app/public/diff/jamaica_sp_list_refs_16243.diff
[CMD] [2019-10-13 21:17:59] tail -n +1 /app/public/converted_csv/jamaica_sp_list_refs_16243.csv >> /app/public/diff/jamaica_sp_list_refs_16243.diff
[CMD] [2019-10-13 21:17:59] echo "." >> /app/public/diff/jamaica_sp_list_refs_16243.diff
[CMD] [2019-10-13 21:17:59] echo "0a" > /app/public/diff/jamaica_sp_list_nodes_16244.diff
[CMD] [2019-10-13 21:17:59] tail -n +1 /app/public/converted_csv/jamaica_sp_list_nodes_16244.csv >> /app/public/diff/jamaica_sp_list_nodes_16244.diff
[CMD] [2019-10-13 21:17:59] echo "." >> /app/public/diff/jamaica_sp_list_nodes_16244.diff
[CMD] [2019-10-13 21:17:59] echo "0a" > /app/public/diff/jamaica_sp_list_occurrences_16245.diff
[CMD] [2019-10-13 21:17:59] tail -n +1 /app/public/converted_csv/jamaica_sp_list_occurrences_16245.csv >> /app/public/diff/jamaica_sp_list_occurrences_16245.diff
[CMD] [2019-10-13 21:17:59] echo "." >> /app/public/diff/jamaica_sp_list_occurrences_16245.diff
[CMD] [2019-10-13 21:18:00] echo "0a" > /app/public/diff/jamaica_sp_list_measurements_16246.diff
[CMD] [2019-10-13 21:18:00] tail -n +1 /app/public/converted_csv/jamaica_sp_list_measurements_16246.csv >> /app/public/diff/jamaica_sp_list_measurements_16246.diff
[CMD] [2019-10-13 21:18:00] echo "." >> /app/public/diff/jamaica_sp_list_measurements_16246.diff
[STOP] [2019-10-13 21:18:00] calculate_delta
[START] [2019-10-13 21:18:00] parse_diff_and_store
[INFO] [2019-10-13 21:18:00] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 21:18:00] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 21:18:04] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 21:18:05] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 21:18:41] Storing 2 References
[INFO] [2019-10-13 21:18:41] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 21:18:41] Average Time: 0.0
[INFO] [2019-10-13 21:18:41] Total Time: 1s
[INFO] [2019-10-13 21:18:41] Storing 10259 ScientificNames
[INFO] [2019-10-13 21:18:41] Processing group of 10259 in 11 groups of 1000
[INFO] [2019-10-13 21:18:45] Average Time: 0.339
[INFO] [2019-10-13 21:18:45] Total Time: 4s
[INFO] [2019-10-13 21:18:45] last 3 / first 3: 0.71
[INFO] [2019-10-13 21:18:45] Std.Dev: 0.08944271909999159; Max: 0.43
[INFO] [2019-10-13 21:18:45] Storing 10259 Nodes
[INFO] [2019-10-13 21:18:45] Processing group of 10259 in 11 groups of 1000
[INFO] [2019-10-13 21:18:48] Average Time: 0.286
[INFO] [2019-10-13 21:18:48] Total Time: 4s
[INFO] [2019-10-13 21:18:48] last 3 / first 3: 0.73
[INFO] [2019-10-13 21:18:48] Std.Dev: 0.07071067811865475; Max: 0.34
[INFO] [2019-10-13 21:18:48] Storing 6266 Occurrences
[INFO] [2019-10-13 21:18:48] Processing group of 6266 in 7 groups of 1000
[INFO] [2019-10-13 21:18:49] Average Time: 0.093
[INFO] [2019-10-13 21:18:49] Total Time: 1s
[INFO] [2019-10-13 21:18:49] last 3 / first 3: 0.72
[INFO] [2019-10-13 21:18:49] Std.Dev: 0.03162277660168379; Max: 0.12
[INFO] [2019-10-13 21:18:49] Storing 12590 TraitsReferences
[INFO] [2019-10-13 21:18:49] Processing group of 12590 in 13 groups of 1000
[INFO] [2019-10-13 21:18:50] Average Time: 0.077
[INFO] [2019-10-13 21:18:50] Total Time: 2s
[INFO] [2019-10-13 21:18:50] last 3 / first 3: 0.6
[INFO] [2019-10-13 21:18:50] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-13 21:18:50] Storing 12589 Traits
[INFO] [2019-10-13 21:18:50] Processing group of 12589 in 13 groups of 1000
[INFO] [2019-10-13 21:18:54] Average Time: 0.337
[INFO] [2019-10-13 21:18:54] Total Time: 5s
[INFO] [2019-10-13 21:18:54] last 3 / first 3: 0.97
[INFO] [2019-10-13 21:18:54] Std.Dev: 0.1; Max: 0.54
[INFO] [2019-10-13 21:18:54] Storing 12575 MetaTraits
[INFO] [2019-10-13 21:18:54] Processing group of 12575 in 13 groups of 1000
[INFO] [2019-10-13 21:18:56] Average Time: 0.112
[INFO] [2019-10-13 21:18:56] Total Time: 2s
[INFO] [2019-10-13 21:18:56] last 3 / first 3: 0.65
[INFO] [2019-10-13 21:18:56] Std.Dev: 0.0; Max: 0.14
[STOP] [2019-10-13 21:18:56] parse_diff_and_store
[START] [2019-10-13 21:18:56] resolve_keys
[INFO] [2019-10-13 21:19:36] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 21:19:39] traits to occurrences...
[INFO] [2019-10-13 21:19:45] traits to nodes (through occurrences)...
[INFO] [2019-10-13 21:19:45] Traits to sex term...
[INFO] [2019-10-13 21:19:49] Traits to lifestage term...
[INFO] [2019-10-13 21:19:53] MetaTraits to traits...
[INFO] [2019-10-13 21:19:53] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 21:19:55] Assocs to occurrences...
[INFO] [2019-10-13 21:19:55] Assocs to nodes...
[INFO] [2019-10-13 21:19:55] Assoc to sex term...
[INFO] [2019-10-13 21:19:55] Assoc to lifestage term...
[STOP] [2019-10-13 21:19:55] resolve_keys
[START] [2019-10-13 21:19:55] hold_for_later_1
[STOP] [2019-10-13 21:19:55] hold_for_later_1
[START] [2019-10-13 21:19:55] hold_for_later_2
[STOP] [2019-10-13 21:19:55] hold_for_later_2
[START] [2019-10-13 21:19:55] resolve_missing_parents
[STOP] [2019-10-13 21:20:16] resolve_missing_parents
[START] [2019-10-13 21:20:16] rebuild_nodes
[START] [2019-10-13 21:20:16] Flattener#flatten
[START] [2019-10-13 21:20:16] Flattener#study_resource
[START] [2019-10-13 21:20:16] Flattener#build_ancestry
[STOP] [2019-10-13 21:20:16] Flattener#build_ancestry
[INFO] [2019-10-13 21:20:16] 10259 ancestry keys
[START] [2019-10-13 21:20:16] build_node_ancestors
[INFO] [2019-10-13 21:20:16] old ancestors deleted.
[STOP] [2019-10-13 21:20:18] build_node_ancestors
[START] [2019-10-13 21:20:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 21:20:21] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 21:20:21] Flattener#flatten
[STOP] [2019-10-13 21:20:21] rebuild_nodes
[START] [2019-10-13 21:20:21] resolve_missing_media_owners
[STOP] [2019-10-13 21:20:21] resolve_missing_media_owners
[START] [2019-10-13 21:20:21] sanitize_media_verbatims
[STOP] [2019-10-13 21:20:21] sanitize_media_verbatims
[START] [2019-10-13 21:20:21] queue_downloads
[STOP] [2019-10-13 21:20:21] queue_downloads
[START] [2019-10-13 21:20:21] parse_names
[WARN] [2019-10-13 21:20:21] I see 10259 names which still need to be parsed.
[STOP] [2019-10-13 21:20:30] parse_names
[START] [2019-10-13 21:20:30] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 21:20:30] denormalize_canonical_names_to_nodes
[START] [2019-10-13 21:20:30] match_nodes
[START] [2019-10-13 21:20:30] map_all_nodes_to_pages
[STOP] [2019-10-13 21:29:38] map_all_nodes_to_pages
[INFO] [2019-10-13 21:29:38] 850 Unmatched nodes (of 10259)! That's too many to output. First 10: Coerebidae (#50403384); Mimus hillii (#50412682); Seiurus aurocapillus (#50410587); Parula (#50404343); Parula americana (#50404342); Dendroica (#50404880); Dendroica petechia (#50404879); Dendroica dominica (#50408378); Dendroica caerulescens (#50412256); Tiaris olivacea (#50405982)
[START] [2019-10-13 21:29:38] update_nodes
[STOP] [2019-10-13 21:29:42] update_nodes
[STOP] [2019-10-13 21:29:42] match_nodes
[START] [2019-10-13 21:29:42] reindex_search
[STOP] [2019-10-13 21:30:05] reindex_search
[START] [2019-10-13 21:30:05] normalize_units
[STOP] [2019-10-13 21:30:05] normalize_units
[START] [2019-10-13 21:30:05] calculate_statistics
[STOP] [2019-10-13 21:30:05] calculate_statistics
[START] [2019-10-13 21:30:05] complete_harvest_instance
[START] [2019-10-13 21:30:05] overall_tsv_creation
[INFO] [2019-10-13 21:30:06] Processing group of 10259 in 2 batches of 10000
[INFO] [2019-10-13 21:31:47] 6104 Traits (unfiltered)...
[INFO] [2019-10-13 21:32:02] 6104 Traits (filtered)...
[INFO] [2019-10-13 21:32:02] 0 Associations (filtered)...
[INFO] [2019-10-13 21:32:55] 30507 metadata added.
[INFO] [2019-10-13 21:32:55] 0 metadata added.
[INFO] [2019-10-13 21:33:40] 162 Traits (unfiltered)...
[INFO] [2019-10-13 21:33:54] 162 Traits (filtered)...
[INFO] [2019-10-13 21:33:54] 0 Associations (filtered)...
[INFO] [2019-10-13 21:34:31] 808 metadata added.
[INFO] [2019-10-13 21:34:31] 0 metadata added.
[INFO] [2019-10-13 21:34:31] Average Time: 109.35
[INFO] [2019-10-13 21:34:31] Total Time: 4m26s
[STOP] [2019-10-13 21:34:31] overall_tsv_creation
[INFO] [2019-10-13 21:34:31] Done. Check your files:
[INFO] [2019-10-13 21:34:31] (10259 lines) /app/public/data/jamaica_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 21:34:32] (32536 lines) /app/public/data/jamaica_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 21:34:32] (10259 lines) /app/public/data/jamaica_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 21:34:32] (6267 lines) /app/public/data/jamaica_sp_list/publish_traits.tsv
[INFO] [2019-10-13 21:34:32] (31316 lines) /app/public/data/jamaica_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 21:34:32] complete_harvest_instance
[START] [2019-10-13 21:34:32] completed
[STOP] [2019-10-13 21:34:32] completed
[STOP] [2019-10-13 21:34:32] logged process, took 997.59
Latest Process

13 Oct 21:17 EXITED currently processing 0