Harvest for ReptileDB Created 03 Jul 13:35

Stage: completed
Fetched: 03 Jul 13:35
Validated: 03 Jul 13:36
Deltas Created 03 Jul 13:36
Units Normalized: 03 Jul 13:41
Ancestry Built: 03 Jul 13:37
Nodes Matched: 03 Jul 13:41
Names Parsed: 03 Jul 13:38
New Models Stored: 03 Jul 13:37
Indexed: 03 Jul 13:41
Completed: 03 Jul 13:45
Time to Harvest: less than a minute
Harvesting Log

(142 lines)
# Logfile created on 2019-07-03 13:35:56 -0400 by logger.rb/56815
[START] [2019-07-03 13:35:56] logged process
[START] [2019-07-03 13:35:56] create_harvest_instance
[STOP] [2019-07-03 13:35:57] create_harvest_instance
[START] [2019-07-03 13:35:57] fetch_files
[STOP] [2019-07-03 13:35:57] fetch_files
[START] [2019-07-03 13:35:57] validate_each_file
[STOP] [2019-07-03 13:36:01] validate_each_file
[START] [2019-07-03 13:36:02] convert_to_csv
[CMD] [2019-07-03 13:36:02] /usr/bin/sort /app/public/converted_csv/reptileDB_agents_13928.csv > /app/public/converted_csv/reptileDB_agents_13928.csv_sorted
[CMD] [2019-07-03 13:36:02] /usr/bin/sort /app/public/converted_csv/reptileDB_nodes_13929.csv > /app/public/converted_csv/reptileDB_nodes_13929.csv_sorted
[CMD] [2019-07-03 13:36:02] /usr/bin/sort /app/public/converted_csv/reptileDB_media_13930.csv > /app/public/converted_csv/reptileDB_media_13930.csv_sorted
[CMD] [2019-07-03 13:36:02] /usr/bin/sort /app/public/converted_csv/reptileDB_vernaculars_13931.csv > /app/public/converted_csv/reptileDB_vernaculars_13931.csv_sorted
[STOP] [2019-07-03 13:36:02] convert_to_csv
[START] [2019-07-03 13:36:02] calculate_delta
[CMD] [2019-07-03 13:36:02] echo "0a" > /app/public/diff/reptileDB_agents_13928.diff
[CMD] [2019-07-03 13:36:02] tail -n +1 /app/public/converted_csv/reptileDB_agents_13928.csv >> /app/public/diff/reptileDB_agents_13928.diff
[CMD] [2019-07-03 13:36:02] echo "." >> /app/public/diff/reptileDB_agents_13928.diff
[CMD] [2019-07-03 13:36:02] echo "0a" > /app/public/diff/reptileDB_nodes_13929.diff
[CMD] [2019-07-03 13:36:02] tail -n +1 /app/public/converted_csv/reptileDB_nodes_13929.csv >> /app/public/diff/reptileDB_nodes_13929.diff
[CMD] [2019-07-03 13:36:02] echo "." >> /app/public/diff/reptileDB_nodes_13929.diff
[CMD] [2019-07-03 13:36:02] echo "0a" > /app/public/diff/reptileDB_media_13930.diff
[CMD] [2019-07-03 13:36:02] tail -n +1 /app/public/converted_csv/reptileDB_media_13930.csv >> /app/public/diff/reptileDB_media_13930.diff
[CMD] [2019-07-03 13:36:02] echo "." >> /app/public/diff/reptileDB_media_13930.diff
[CMD] [2019-07-03 13:36:02] echo "0a" > /app/public/diff/reptileDB_vernaculars_13931.diff
[CMD] [2019-07-03 13:36:02] tail -n +1 /app/public/converted_csv/reptileDB_vernaculars_13931.csv >> /app/public/diff/reptileDB_vernaculars_13931.diff
[CMD] [2019-07-03 13:36:02] echo "." >> /app/public/diff/reptileDB_vernaculars_13931.diff
[STOP] [2019-07-03 13:36:02] calculate_delta
[START] [2019-07-03 13:36:02] parse_diff_and_store
[INFO] [2019-07-03 13:36:02] Loading agents diff file into memory (true lines)...
[INFO] [2019-07-03 13:36:02] Loading nodes diff file into memory (true lines)...
[INFO] [2019-07-03 13:36:22] Loading media diff file into memory (true lines)...
[INFO] [2019-07-03 13:36:33] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-07-03 13:36:35] Storing 1 Attributions
[INFO] [2019-07-03 13:36:35] Processing group of 1 in 1 groups of 1000
[INFO] [2019-07-03 13:36:35] Average Time: 0.01
[INFO] [2019-07-03 13:36:35] Total Time: 1s
[INFO] [2019-07-03 13:36:35] Storing 73365 ScientificNames
[INFO] [2019-07-03 13:36:35] Processing group of 73365 in 74 groups of 1000
[INFO] [2019-07-03 13:37:04] Average Time: 0.383
[INFO] [2019-07-03 13:37:04] Total Time: 29s
[INFO] [2019-07-03 13:37:04] last 3 / first 3: 0.72
[INFO] [2019-07-03 13:37:04] Std.Dev: 0.08944271909999159; Max: 0.8
[INFO] [2019-07-03 13:37:04] Storing 10548 Nodes
[INFO] [2019-07-03 13:37:04] Processing group of 10548 in 11 groups of 1000
[INFO] [2019-07-03 13:37:07] Average Time: 0.335
[INFO] [2019-07-03 13:37:07] Total Time: 4s
[INFO] [2019-07-03 13:37:07] last 3 / first 3: 0.54
[INFO] [2019-07-03 13:37:07] Std.Dev: 0.17029386365926402; Max: 0.84
[INFO] [2019-07-03 13:37:07] Storing 9362 ArticlesSections
[INFO] [2019-07-03 13:37:07] Processing group of 9362 in 10 groups of 1000
[INFO] [2019-07-03 13:37:08] Average Time: 0.055
[INFO] [2019-07-03 13:37:08] Total Time: 1s
[INFO] [2019-07-03 13:37:08] last 3 / first 3: 0.82
[INFO] [2019-07-03 13:37:08] Std.Dev: 0.0; Max: 0.06
[INFO] [2019-07-03 13:37:08] Storing 9362 Articles
[INFO] [2019-07-03 13:37:08] Processing group of 9362 in 10 groups of 1000
[INFO] [2019-07-03 13:37:11] Average Time: 0.29
[INFO] [2019-07-03 13:37:11] Total Time: 3s
[INFO] [2019-07-03 13:37:11] last 3 / first 3: 0.83
[INFO] [2019-07-03 13:37:11] Std.Dev: 0.05477225575051661; Max: 0.33
[INFO] [2019-07-03 13:37:11] Storing 10239 Vernaculars
[INFO] [2019-07-03 13:37:11] Processing group of 10239 in 11 groups of 1000
[INFO] [2019-07-03 13:37:14] Average Time: 0.27
[INFO] [2019-07-03 13:37:14] Total Time: 4s
[INFO] [2019-07-03 13:37:14] last 3 / first 3: 0.48
[INFO] [2019-07-03 13:37:14] Std.Dev: 0.13784048752090222; Max: 0.61
[STOP] [2019-07-03 13:37:14] parse_diff_and_store
[START] [2019-07-03 13:37:14] resolve_keys
[INFO] [2019-07-03 13:37:29] Occurrences to nodes (through scientific_names)...
[INFO] [2019-07-03 13:37:29] traits to occurrences...
[INFO] [2019-07-03 13:37:29] traits to nodes (through occurrences)...
[INFO] [2019-07-03 13:37:29] Traits to sex term...
[INFO] [2019-07-03 13:37:29] Traits to lifestage term...
[INFO] [2019-07-03 13:37:29] MetaTraits to traits...
[INFO] [2019-07-03 13:37:29] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-07-03 13:37:29] Assocs to occurrences...
[INFO] [2019-07-03 13:37:29] Assocs to nodes...
[INFO] [2019-07-03 13:37:29] Assoc to sex term...
[INFO] [2019-07-03 13:37:29] Assoc to lifestage term...
[STOP] [2019-07-03 13:37:29] resolve_keys
[START] [2019-07-03 13:37:29] hold_for_later_1
[STOP] [2019-07-03 13:37:29] hold_for_later_1
[START] [2019-07-03 13:37:29] hold_for_later_2
[STOP] [2019-07-03 13:37:29] hold_for_later_2
[START] [2019-07-03 13:37:29] resolve_missing_parents
[STOP] [2019-07-03 13:37:29] resolve_missing_parents
[START] [2019-07-03 13:37:29] rebuild_nodes
[START] [2019-07-03 13:37:29] Flattener#flatten
[START] [2019-07-03 13:37:29] Flattener#study_resource
[START] [2019-07-03 13:37:29] Flattener#build_ancestry
[STOP] [2019-07-03 13:37:31] Flattener#build_ancestry
[INFO] [2019-07-03 13:37:31] 10548 ancestry keys
[START] [2019-07-03 13:37:31] build_node_ancestors
[INFO] [2019-07-03 13:37:31] old ancestors deleted.
[STOP] [2019-07-03 13:37:32] build_node_ancestors
[START] [2019-07-03 13:37:34] Flattener#propagate_ancestor_ids
[STOP] [2019-07-03 13:37:34] Flattener#propagate_ancestor_ids
[STOP] [2019-07-03 13:37:34] Flattener#flatten
[STOP] [2019-07-03 13:37:34] rebuild_nodes
[START] [2019-07-03 13:37:34] resolve_missing_media_owners
[STOP] [2019-07-03 13:37:34] resolve_missing_media_owners
[START] [2019-07-03 13:37:34] sanitize_media_verbatims
[STOP] [2019-07-03 13:37:34] sanitize_media_verbatims
[START] [2019-07-03 13:37:34] queue_downloads
[STOP] [2019-07-03 13:37:34] queue_downloads
[START] [2019-07-03 13:37:34] parse_names
[WARN] [2019-07-03 13:37:34] I see 73365 names which still need to be parsed.
[WARN] [2019-07-03 13:38:36] I see 578 names which still need to be parsed.
[STOP] [2019-07-03 13:38:38] parse_names
[START] [2019-07-03 13:38:38] denormalize_canonical_names_to_nodes
[STOP] [2019-07-03 13:38:38] denormalize_canonical_names_to_nodes
[START] [2019-07-03 13:38:38] match_nodes
[START] [2019-07-03 13:38:38] map_all_nodes_to_pages
[STOP] [2019-07-03 13:41:21] map_all_nodes_to_pages
[INFO] [2019-07-03 13:41:21] 572 Unmatched nodes (of 10548)! That's too many to output. First 10: Ablepharis (#44034838); Brachymeles gracilis gracilis (#44036378); Emoa (#44038236); Lerista orentialis (#44039796); Egernia geophana (#44040121); Eumeces punctatus (#44040380); Campsodactylus (#44040388); Eumeces mabouia (#44040417); Mabuya mabouya sloani (#44040418); Eumeces sloanii (#44040423)
[START] [2019-07-03 13:41:21] update_nodes
[STOP] [2019-07-03 13:41:25] update_nodes
[STOP] [2019-07-03 13:41:25] match_nodes
[START] [2019-07-03 13:41:25] reindex_search
[STOP] [2019-07-03 13:41:49] reindex_search
[START] [2019-07-03 13:41:49] normalize_units
[STOP] [2019-07-03 13:41:49] normalize_units
[START] [2019-07-03 13:41:49] calculate_statistics
[STOP] [2019-07-03 13:41:49] calculate_statistics
[START] [2019-07-03 13:41:49] complete_harvest_instance
[START] [2019-07-03 13:41:49] overall_tsv_creation
[INFO] [2019-07-03 13:41:49] Processing group of 10548 in 2 batches of 10000
[INFO] [2019-07-03 13:45:44] Average Time: 83.41
[INFO] [2019-07-03 13:45:44] Total Time: 3m56s
[STOP] [2019-07-03 13:45:44] overall_tsv_creation
[INFO] [2019-07-03 13:45:44] Done. Check your files:
[INFO] [2019-07-03 13:45:45] (10548 lines) /app/public/data/reptileDB/publish_nodes.tsv
[INFO] [2019-07-03 13:45:45] (19833 lines) /app/public/data/reptileDB/publish_node_ancestors.tsv
[INFO] [2019-07-03 13:45:45] (73365 lines) /app/public/data/reptileDB/publish_scientific_names.tsv
[INFO] [2019-07-03 13:45:45] (9362 lines) /app/public/data/reptileDB/publish_articles.tsv
[INFO] [2019-07-03 13:45:45] (9792 lines) /app/public/data/reptileDB/publish_vernaculars.tsv
[INFO] [2019-07-03 13:45:45] (9362 lines) /app/public/data/reptileDB/publish_content_sections.tsv
[STOP] [2019-07-03 13:45:45] complete_harvest_instance
[START] [2019-07-03 13:45:45] completed
[STOP] [2019-07-03 13:45:45] completed
[STOP] [2019-07-03 13:45:45] logged process, took 588.66
Latest Process

03 Jul 13:35 EXITED currently processing 0