Harvest for Armenia Species List Created 01 Oct 18:59

Stage: completed
Fetched: 01 Oct 18:59
Validated: 01 Oct 18:59
Deltas Created 01 Oct 19:00
Units Normalized: 01 Oct 19:06
Ancestry Built: 01 Oct 19:01
Nodes Matched: 01 Oct 19:06
Names Parsed: 01 Oct 19:01
New Models Stored: 01 Oct 19:00
Indexed: 01 Oct 19:06
Completed: 01 Oct 19:08
Time to Harvest: less than a minute

Expected File Format Definitions

Harvesting Log (most recent first)

# Logfile created on 2019-10-01 18:59:42 -0400 by logger.rb/56815
[START] [2019-10-01 18:59:42] logged process
[START] [2019-10-01 18:59:42] create_harvest_instance
[STOP] [2019-10-01 18:59:42] create_harvest_instance
[START] [2019-10-01 18:59:42] fetch_files
[STOP] [2019-10-01 18:59:42] fetch_files
[START] [2019-10-01 18:59:42] validate_each_file
[STOP] [2019-10-01 18:59:44] validate_each_file
[START] [2019-10-01 18:59:44] convert_to_csv
[CMD] [2019-10-01 18:59:44] /usr/bin/sort /app/public/converted_csv/armenia_sp_list_refs_14828.csv > /app/public/converted_csv/armenia_sp_list_refs_14828.csv_sorted
[CMD] [2019-10-01 18:59:45] /usr/bin/sort /app/public/converted_csv/armenia_sp_list_nodes_14829.csv > /app/public/converted_csv/armenia_sp_list_nodes_14829.csv_sorted
[CMD] [2019-10-01 18:59:47] /usr/bin/sort /app/public/converted_csv/armenia_sp_list_occurrences_14830.csv > /app/public/converted_csv/armenia_sp_list_occurrences_14830.csv_sorted
[CMD] [2019-10-01 18:59:48] /usr/bin/sort /app/public/converted_csv/armenia_sp_list_measurements_14831.csv > /app/public/converted_csv/armenia_sp_list_measurements_14831.csv_sorted
[STOP] [2019-10-01 18:59:50] convert_to_csv
[START] [2019-10-01 18:59:50] calculate_delta
[CMD] [2019-10-01 18:59:50] echo "0a" > /app/public/diff/armenia_sp_list_refs_14828.diff
[CMD] [2019-10-01 18:59:51] tail -n +1 /app/public/converted_csv/armenia_sp_list_refs_14828.csv >> /app/public/diff/armenia_sp_list_refs_14828.diff
[CMD] [2019-10-01 18:59:53] echo "." >> /app/public/diff/armenia_sp_list_refs_14828.diff
[CMD] [2019-10-01 18:59:54] echo "0a" > /app/public/diff/armenia_sp_list_nodes_14829.diff
[CMD] [2019-10-01 18:59:56] tail -n +1 /app/public/converted_csv/armenia_sp_list_nodes_14829.csv >> /app/public/diff/armenia_sp_list_nodes_14829.diff
[CMD] [2019-10-01 18:59:57] echo "." >> /app/public/diff/armenia_sp_list_nodes_14829.diff
[CMD] [2019-10-01 18:59:59] echo "0a" > /app/public/diff/armenia_sp_list_occurrences_14830.diff
[CMD] [2019-10-01 19:00:00] tail -n +1 /app/public/converted_csv/armenia_sp_list_occurrences_14830.csv >> /app/public/diff/armenia_sp_list_occurrences_14830.diff
[CMD] [2019-10-01 19:00:02] echo "." >> /app/public/diff/armenia_sp_list_occurrences_14830.diff
[CMD] [2019-10-01 19:00:04] echo "0a" > /app/public/diff/armenia_sp_list_measurements_14831.diff
[CMD] [2019-10-01 19:00:05] tail -n +1 /app/public/converted_csv/armenia_sp_list_measurements_14831.csv >> /app/public/diff/armenia_sp_list_measurements_14831.diff
[CMD] [2019-10-01 19:00:07] echo "." >> /app/public/diff/armenia_sp_list_measurements_14831.diff
[STOP] [2019-10-01 19:00:08] calculate_delta
[START] [2019-10-01 19:00:08] parse_diff_and_store
[INFO] [2019-10-01 19:00:10] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-01 19:00:11] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-01 19:00:14] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-01 19:00:16] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-01 19:00:38] Storing 2 References
[INFO] [2019-10-01 19:00:38] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-01 19:00:38] Average Time: 0.0
[INFO] [2019-10-01 19:00:38] Total Time: 1s
[INFO] [2019-10-01 19:00:38] Storing 5787 ScientificNames
[INFO] [2019-10-01 19:00:38] Processing group of 5787 in 6 groups of 1000
[INFO] [2019-10-01 19:00:40] Average Time: 0.335
[INFO] [2019-10-01 19:00:40] Total Time: 3s
[INFO] [2019-10-01 19:00:40] Storing 5787 Nodes
[INFO] [2019-10-01 19:00:40] Processing group of 5787 in 6 groups of 1000
[INFO] [2019-10-01 19:00:42] Average Time: 0.273
[INFO] [2019-10-01 19:00:42] Total Time: 2s
[INFO] [2019-10-01 19:00:42] Storing 3856 Occurrences
[INFO] [2019-10-01 19:00:42] Processing group of 3856 in 4 groups of 1000
[INFO] [2019-10-01 19:00:42] Average Time: 0.095
[INFO] [2019-10-01 19:00:42] Total Time: 1s
[INFO] [2019-10-01 19:00:42] Storing 8112 TraitsReferences
[INFO] [2019-10-01 19:00:42] Processing group of 8112 in 9 groups of 1000
[INFO] [2019-10-01 19:00:43] Average Time: 0.07
[INFO] [2019-10-01 19:00:43] Total Time: 1s
[INFO] [2019-10-01 19:00:43] last 3 / first 3: 0.47
[INFO] [2019-10-01 19:00:43] Std.Dev: 0.03162277660168379; Max: 0.14
[INFO] [2019-10-01 19:00:43] Storing 8111 Traits
[INFO] [2019-10-01 19:00:43] Processing group of 8111 in 9 groups of 1000
[INFO] [2019-10-01 19:00:45] Average Time: 0.271
[INFO] [2019-10-01 19:00:45] Total Time: 3s
[INFO] [2019-10-01 19:00:45] last 3 / first 3: 0.68
[INFO] [2019-10-01 19:00:45] Std.Dev: 0.08944271909999159; Max: 0.36
[INFO] [2019-10-01 19:00:45] Storing 8111 MetaTraits
[INFO] [2019-10-01 19:00:45] Processing group of 8111 in 9 groups of 1000
[INFO] [2019-10-01 19:00:47] Average Time: 0.153
[INFO] [2019-10-01 19:00:47] Total Time: 2s
[INFO] [2019-10-01 19:00:47] last 3 / first 3: 1.28
[INFO] [2019-10-01 19:00:47] Std.Dev: 0.09486832980505137; Max: 0.37
[STOP] [2019-10-01 19:00:47] parse_diff_and_store
[START] [2019-10-01 19:00:47] resolve_keys
[INFO] [2019-10-01 19:01:14] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-01 19:01:17] traits to occurrences...
[INFO] [2019-10-01 19:01:18] traits to nodes (through occurrences)...
[INFO] [2019-10-01 19:01:19] Traits to sex term...
[INFO] [2019-10-01 19:01:20] Traits to lifestage term...
[INFO] [2019-10-01 19:01:21] MetaTraits to traits...
[INFO] [2019-10-01 19:01:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-01 19:01:23] Assocs to occurrences...
[INFO] [2019-10-01 19:01:23] Assocs to nodes...
[INFO] [2019-10-01 19:01:23] Assoc to sex term...
[INFO] [2019-10-01 19:01:23] Assoc to lifestage term...
[STOP] [2019-10-01 19:01:23] resolve_keys
[START] [2019-10-01 19:01:23] hold_for_later_1
[STOP] [2019-10-01 19:01:23] hold_for_later_1
[START] [2019-10-01 19:01:23] hold_for_later_2
[STOP] [2019-10-01 19:01:23] hold_for_later_2
[START] [2019-10-01 19:01:23] resolve_missing_parents
[STOP] [2019-10-01 19:01:36] resolve_missing_parents
[START] [2019-10-01 19:01:36] rebuild_nodes
[START] [2019-10-01 19:01:36] Flattener#flatten
[START] [2019-10-01 19:01:36] Flattener#study_resource
[START] [2019-10-01 19:01:36] Flattener#build_ancestry
[STOP] [2019-10-01 19:01:37] Flattener#build_ancestry
[INFO] [2019-10-01 19:01:37] 5787 ancestry keys
[START] [2019-10-01 19:01:37] build_node_ancestors
[INFO] [2019-10-01 19:01:37] old ancestors deleted.
[STOP] [2019-10-01 19:01:37] build_node_ancestors
[START] [2019-10-01 19:01:39] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 19:01:39] Flattener#propagate_ancestor_ids
[STOP] [2019-10-01 19:01:39] Flattener#flatten
[STOP] [2019-10-01 19:01:39] rebuild_nodes
[START] [2019-10-01 19:01:39] resolve_missing_media_owners
[STOP] [2019-10-01 19:01:39] resolve_missing_media_owners
[START] [2019-10-01 19:01:39] sanitize_media_verbatims
[STOP] [2019-10-01 19:01:39] sanitize_media_verbatims
[START] [2019-10-01 19:01:39] queue_downloads
[STOP] [2019-10-01 19:01:39] queue_downloads
[START] [2019-10-01 19:01:39] parse_names
[WARN] [2019-10-01 19:01:39] I see 5787 names which still need to be parsed.
[STOP] [2019-10-01 19:01:44] parse_names
[START] [2019-10-01 19:01:44] denormalize_canonical_names_to_nodes
[STOP] [2019-10-01 19:01:44] denormalize_canonical_names_to_nodes
[START] [2019-10-01 19:01:44] match_nodes
[START] [2019-10-01 19:01:44] map_all_nodes_to_pages
[STOP] [2019-10-01 19:06:16] map_all_nodes_to_pages
[INFO] [2019-10-01 19:06:16] 398 Unmatched nodes (of 5787)! That's too many to output. First 10: Paralaudakia caucasica (#47447716); Vipera raddei (#47448509); Carduelis cannabina (#47446858); Carduelis flavirostris (#47448036); Parus lugubris (#47450986); Parus caeruleus (#47451814); Erythropygia (#47450729); Erythropygia galactotes (#47450728); Corvus monedula (#47447269); Phylloscopus lorenzii (#47450755)
[START] [2019-10-01 19:06:16] update_nodes
[STOP] [2019-10-01 19:06:18] update_nodes
[STOP] [2019-10-01 19:06:18] match_nodes
[START] [2019-10-01 19:06:18] reindex_search
[STOP] [2019-10-01 19:06:33] reindex_search
[START] [2019-10-01 19:06:33] normalize_units
[STOP] [2019-10-01 19:06:33] normalize_units
[START] [2019-10-01 19:06:33] calculate_statistics
[STOP] [2019-10-01 19:06:33] calculate_statistics
[START] [2019-10-01 19:06:33] complete_harvest_instance
[START] [2019-10-01 19:06:33] overall_tsv_creation
[INFO] [2019-10-01 19:06:33] Processing group of 5787 in 1 batches of 10000
[INFO] [2019-10-01 19:07:40] 3856 Traits (unfiltered)...
[INFO] [2019-10-01 19:07:53] 3856 Traits (filtered)...
[INFO] [2019-10-01 19:07:53] 0 Associations (filtered)...
[INFO] [2019-10-01 19:08:35] 19279 metadata added.
[INFO] [2019-10-01 19:08:35] 0 metadata added.
[INFO] [2019-10-01 19:08:35] Average Time: 97.67
[INFO] [2019-10-01 19:08:35] Total Time: 2m2s
[STOP] [2019-10-01 19:08:35] overall_tsv_creation
[INFO] [2019-10-01 19:08:35] Done. Check your files:
[INFO] [2019-10-01 19:08:36] (5787 lines) /app/public/data/armenia_sp_list/publish_nodes.tsv
[INFO] [2019-10-01 19:08:38] (14773 lines) /app/public/data/armenia_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-01 19:08:39] (5787 lines) /app/public/data/armenia_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-01 19:08:41] (3857 lines) /app/public/data/armenia_sp_list/publish_traits.tsv
[INFO] [2019-10-01 19:08:42] (19280 lines) /app/public/data/armenia_sp_list/publish_metadata.tsv
[STOP] [2019-10-01 19:08:43] complete_harvest_instance
[START] [2019-10-01 19:08:43] completed
[STOP] [2019-10-01 19:08:43] completed
[STOP] [2019-10-01 19:08:43] logged process, took 540.62

Latest Process