Harvest for Chile Species List Created 12 Oct 02:41

Stage: completed
Fetched: 12 Oct 02:41
Validated: 12 Oct 02:41
Deltas Created 12 Oct 02:41
Units Normalized: 12 Oct 03:07
Ancestry Built: 12 Oct 02:46
Nodes Matched: 12 Oct 03:06
Names Parsed: 12 Oct 02:46
New Models Stored: 12 Oct 02:43
Indexed: 12 Oct 03:07
Completed: 12 Oct 03:15
Time to Harvest: 1 minute
Harvesting Log

(161 lines)
# Logfile created on 2019-10-12 02:41:20 -0400 by logger.rb/56815
[START] [2019-10-12 02:41:20] logged process
[START] [2019-10-12 02:41:20] create_harvest_instance
[STOP] [2019-10-12 02:41:21] create_harvest_instance
[START] [2019-10-12 02:41:21] fetch_files
[STOP] [2019-10-12 02:41:21] fetch_files
[START] [2019-10-12 02:41:21] validate_each_file
[STOP] [2019-10-12 02:41:24] validate_each_file
[START] [2019-10-12 02:41:24] convert_to_csv
[CMD] [2019-10-12 02:41:24] /usr/bin/sort /app/public/converted_csv/chile_sp_list_refs_15419.csv > /app/public/converted_csv/chile_sp_list_refs_15419.csv_sorted
[CMD] [2019-10-12 02:41:24] /usr/bin/sort /app/public/converted_csv/chile_sp_list_nodes_15420.csv > /app/public/converted_csv/chile_sp_list_nodes_15420.csv_sorted
[CMD] [2019-10-12 02:41:24] /usr/bin/sort /app/public/converted_csv/chile_sp_list_occurrences_15421.csv > /app/public/converted_csv/chile_sp_list_occurrences_15421.csv_sorted
[CMD] [2019-10-12 02:41:24] /usr/bin/sort /app/public/converted_csv/chile_sp_list_measurements_15422.csv > /app/public/converted_csv/chile_sp_list_measurements_15422.csv_sorted
[STOP] [2019-10-12 02:41:24] convert_to_csv
[START] [2019-10-12 02:41:24] calculate_delta
[CMD] [2019-10-12 02:41:24] echo "0a" > /app/public/diff/chile_sp_list_refs_15419.diff
[CMD] [2019-10-12 02:41:24] tail -n +1 /app/public/converted_csv/chile_sp_list_refs_15419.csv >> /app/public/diff/chile_sp_list_refs_15419.diff
[CMD] [2019-10-12 02:41:24] echo "." >> /app/public/diff/chile_sp_list_refs_15419.diff
[CMD] [2019-10-12 02:41:24] echo "0a" > /app/public/diff/chile_sp_list_nodes_15420.diff
[CMD] [2019-10-12 02:41:24] tail -n +1 /app/public/converted_csv/chile_sp_list_nodes_15420.csv >> /app/public/diff/chile_sp_list_nodes_15420.diff
[CMD] [2019-10-12 02:41:24] echo "." >> /app/public/diff/chile_sp_list_nodes_15420.diff
[CMD] [2019-10-12 02:41:25] echo "0a" > /app/public/diff/chile_sp_list_occurrences_15421.diff
[CMD] [2019-10-12 02:41:25] tail -n +1 /app/public/converted_csv/chile_sp_list_occurrences_15421.csv >> /app/public/diff/chile_sp_list_occurrences_15421.diff
[CMD] [2019-10-12 02:41:25] echo "." >> /app/public/diff/chile_sp_list_occurrences_15421.diff
[CMD] [2019-10-12 02:41:25] echo "0a" > /app/public/diff/chile_sp_list_measurements_15422.diff
[CMD] [2019-10-12 02:41:25] tail -n +1 /app/public/converted_csv/chile_sp_list_measurements_15422.csv >> /app/public/diff/chile_sp_list_measurements_15422.diff
[CMD] [2019-10-12 02:41:25] echo "." >> /app/public/diff/chile_sp_list_measurements_15422.diff
[STOP] [2019-10-12 02:41:25] calculate_delta
[START] [2019-10-12 02:41:25] parse_diff_and_store
[INFO] [2019-10-12 02:41:25] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 02:41:25] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 02:41:35] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 02:41:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 02:43:07] Storing 2 References
[INFO] [2019-10-12 02:43:07] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 02:43:07] Average Time: 0.0
[INFO] [2019-10-12 02:43:07] Total Time: 1s
[INFO] [2019-10-12 02:43:07] Storing 23476 ScientificNames
[INFO] [2019-10-12 02:43:07] Processing group of 23476 in 24 groups of 1000
[INFO] [2019-10-12 02:43:15] Average Time: 0.353
[INFO] [2019-10-12 02:43:15] Total Time: 9s
[INFO] [2019-10-12 02:43:15] last 3 / first 3: 0.77
[INFO] [2019-10-12 02:43:15] Std.Dev: 0.05477225575051661; Max: 0.5
[INFO] [2019-10-12 02:43:15] Storing 23476 Nodes
[INFO] [2019-10-12 02:43:15] Processing group of 23476 in 24 groups of 1000
[INFO] [2019-10-12 02:43:23] Average Time: 0.323
[INFO] [2019-10-12 02:43:23] Total Time: 8s
[INFO] [2019-10-12 02:43:23] last 3 / first 3: 0.8
[INFO] [2019-10-12 02:43:23] Std.Dev: 0.12649110640673517; Max: 0.76
[INFO] [2019-10-12 02:43:23] Storing 15424 Occurrences
[INFO] [2019-10-12 02:43:23] Processing group of 15424 in 16 groups of 1000
[INFO] [2019-10-12 02:43:25] Average Time: 0.101
[INFO] [2019-10-12 02:43:25] Total Time: 2s
[INFO] [2019-10-12 02:43:25] last 3 / first 3: 0.83
[INFO] [2019-10-12 02:43:25] Std.Dev: 0.03162277660168379; Max: 0.16
[INFO] [2019-10-12 02:43:25] Storing 31152 TraitsReferences
[INFO] [2019-10-12 02:43:25] Processing group of 31152 in 32 groups of 1000
[INFO] [2019-10-12 02:43:27] Average Time: 0.071
[INFO] [2019-10-12 02:43:27] Total Time: 3s
[INFO] [2019-10-12 02:43:27] last 3 / first 3: 0.54
[INFO] [2019-10-12 02:43:27] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-10-12 02:43:27] Storing 31151 Traits
[INFO] [2019-10-12 02:43:27] Processing group of 31151 in 32 groups of 1000
[INFO] [2019-10-12 02:43:37] Average Time: 0.297
[INFO] [2019-10-12 02:43:37] Total Time: 10s
[INFO] [2019-10-12 02:43:37] last 3 / first 3: 0.71
[INFO] [2019-10-12 02:43:37] Std.Dev: 0.05477225575051661; Max: 0.42
[INFO] [2019-10-12 02:43:37] Storing 31112 MetaTraits
[INFO] [2019-10-12 02:43:37] Processing group of 31112 in 32 groups of 1000
[INFO] [2019-10-12 02:43:42] Average Time: 0.166
[INFO] [2019-10-12 02:43:42] Total Time: 6s
[INFO] [2019-10-12 02:43:42] last 3 / first 3: 0.75
[INFO] [2019-10-12 02:43:42] Std.Dev: 0.11401754250991379; Max: 0.71
[STOP] [2019-10-12 02:43:42] parse_diff_and_store
[START] [2019-10-12 02:43:42] resolve_keys
[INFO] [2019-10-12 02:44:55] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 02:45:01] traits to occurrences...
[INFO] [2019-10-12 02:45:06] traits to nodes (through occurrences)...
[INFO] [2019-10-12 02:45:06] Traits to sex term...
[INFO] [2019-10-12 02:45:11] Traits to lifestage term...
[INFO] [2019-10-12 02:45:17] MetaTraits to traits...
[INFO] [2019-10-12 02:45:19] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 02:45:23] Assocs to occurrences...
[INFO] [2019-10-12 02:45:23] Assocs to nodes...
[INFO] [2019-10-12 02:45:23] Assoc to sex term...
[INFO] [2019-10-12 02:45:23] Assoc to lifestage term...
[STOP] [2019-10-12 02:45:23] resolve_keys
[START] [2019-10-12 02:45:23] hold_for_later_1
[STOP] [2019-10-12 02:45:23] hold_for_later_1
[START] [2019-10-12 02:45:23] hold_for_later_2
[STOP] [2019-10-12 02:45:23] hold_for_later_2
[START] [2019-10-12 02:45:23] resolve_missing_parents
[STOP] [2019-10-12 02:46:09] resolve_missing_parents
[START] [2019-10-12 02:46:09] rebuild_nodes
[START] [2019-10-12 02:46:09] Flattener#flatten
[START] [2019-10-12 02:46:09] Flattener#study_resource
[START] [2019-10-12 02:46:10] Flattener#build_ancestry
[STOP] [2019-10-12 02:46:11] Flattener#build_ancestry
[INFO] [2019-10-12 02:46:11] 23476 ancestry keys
[START] [2019-10-12 02:46:11] build_node_ancestors
[INFO] [2019-10-12 02:46:11] old ancestors deleted.
[STOP] [2019-10-12 02:46:18] build_node_ancestors
[START] [2019-10-12 02:46:25] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:46:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 02:46:28] Flattener#flatten
[STOP] [2019-10-12 02:46:28] rebuild_nodes
[START] [2019-10-12 02:46:28] resolve_missing_media_owners
[STOP] [2019-10-12 02:46:28] resolve_missing_media_owners
[START] [2019-10-12 02:46:28] sanitize_media_verbatims
[STOP] [2019-10-12 02:46:28] sanitize_media_verbatims
[START] [2019-10-12 02:46:28] queue_downloads
[STOP] [2019-10-12 02:46:28] queue_downloads
[START] [2019-10-12 02:46:28] parse_names
[WARN] [2019-10-12 02:46:28] I see 23476 names which still need to be parsed.
[STOP] [2019-10-12 02:46:46] parse_names
[START] [2019-10-12 02:46:46] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 02:46:46] denormalize_canonical_names_to_nodes
[START] [2019-10-12 02:46:46] match_nodes
[START] [2019-10-12 02:46:46] map_all_nodes_to_pages
[STOP] [2019-10-12 03:06:44] map_all_nodes_to_pages
[INFO] [2019-10-12 03:06:44] 2214 Unmatched nodes (of 23476)! That's too many to output. First 10: Falco kreyenborgi (#49110504); Charadrius occidentalis (#49116623); Chlidonias nigra (#49107091); Thalaseus (#49099684); Thalaseus elegans (#49099683); Thalaseus sandvicensis (#49101331); Rynchops nigra (#49106739); Onychoprion fuscata (#49108947); Tringa semipalmatus (#49104921); Aphriza (#49101184)
[START] [2019-10-12 03:06:44] update_nodes
[STOP] [2019-10-12 03:06:52] update_nodes
[STOP] [2019-10-12 03:06:52] match_nodes
[START] [2019-10-12 03:06:52] reindex_search
[STOP] [2019-10-12 03:07:53] reindex_search
[START] [2019-10-12 03:07:53] normalize_units
[STOP] [2019-10-12 03:07:53] normalize_units
[START] [2019-10-12 03:07:53] calculate_statistics
[STOP] [2019-10-12 03:07:53] calculate_statistics
[START] [2019-10-12 03:07:53] complete_harvest_instance
[START] [2019-10-12 03:07:53] overall_tsv_creation
[INFO] [2019-10-12 03:07:53] Processing group of 23476 in 3 batches of 10000
[INFO] [2019-10-12 03:09:22] 5698 Traits (unfiltered)...
[INFO] [2019-10-12 03:09:36] 5698 Traits (filtered)...
[INFO] [2019-10-12 03:09:36] 0 Associations (filtered)...
[INFO] [2019-10-12 03:10:24] 28482 metadata added.
[INFO] [2019-10-12 03:10:24] 0 metadata added.
[INFO] [2019-10-12 03:11:56] 7046 Traits (unfiltered)...
[INFO] [2019-10-12 03:12:10] 7046 Traits (filtered)...
[INFO] [2019-10-12 03:12:10] 0 Associations (filtered)...
[INFO] [2019-10-12 03:13:04] 35213 metadata added.
[INFO] [2019-10-12 03:13:04] 0 metadata added.
[INFO] [2019-10-12 03:14:07] 2680 Traits (unfiltered)...
[INFO] [2019-10-12 03:14:20] 2680 Traits (filtered)...
[INFO] [2019-10-12 03:14:21] 0 Associations (filtered)...
[INFO] [2019-10-12 03:15:03] 13385 metadata added.
[INFO] [2019-10-12 03:15:03] 0 metadata added.
[INFO] [2019-10-12 03:15:03] Average Time: 117.753
[INFO] [2019-10-12 03:15:03] Total Time: 7m10s
[STOP] [2019-10-12 03:15:03] overall_tsv_creation
[INFO] [2019-10-12 03:15:03] Done. Check your files:
[INFO] [2019-10-12 03:15:03] (23476 lines) /app/public/data/chile_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 03:15:03] (90175 lines) /app/public/data/chile_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 03:15:03] (23476 lines) /app/public/data/chile_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 03:15:03] (15425 lines) /app/public/data/chile_sp_list/publish_traits.tsv
[INFO] [2019-10-12 03:15:03] (77081 lines) /app/public/data/chile_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 03:15:03] complete_harvest_instance
[START] [2019-10-12 03:15:03] completed
[STOP] [2019-10-12 03:15:03] completed
[STOP] [2019-10-12 03:15:03] logged process, took 2023.09
Latest Process

12 Oct 02:41 EXITED currently processing 0