Harvest for The Fish Database of Taiwan Created 31 Dec 10:08

Harvesting Log

# Logfile created on 2019-12-31 10:08:32 -0500 by logger.rb/56815
[START] [2019-12-31 10:08:32] logged process
[START] [2019-12-31 10:08:32] create_harvest_instance
[STOP] [2019-12-31 10:08:33] create_harvest_instance
[START] [2019-12-31 10:08:33] fetch_files
[STOP] [2019-12-31 10:08:33] fetch_files
[START] [2019-12-31 10:08:33] validate_each_file
[STOP] [2019-12-31 10:08:35] validate_each_file
[START] [2019-12-31 10:08:35] convert_to_csv
[CMD] [2019-12-31 10:08:35] /usr/bin/sort /app/public/converted_csv/fdtdt_agents_19813.csv > /app/public/converted_csv/fdtdt_agents_19813.csv_sorted
[CMD] [2019-12-31 10:08:36] /usr/bin/sort /app/public/converted_csv/fdtdt_nodes_19814.csv > /app/public/converted_csv/fdtdt_nodes_19814.csv_sorted
[CMD] [2019-12-31 10:08:36] /usr/bin/sort /app/public/converted_csv/fdtdt_media_19815.csv > /app/public/converted_csv/fdtdt_media_19815.csv_sorted
[CMD] [2019-12-31 10:08:37] /usr/bin/sort /app/public/converted_csv/fdtdt_vernaculars_19816.csv > /app/public/converted_csv/fdtdt_vernaculars_19816.csv_sorted
[STOP] [2019-12-31 10:08:37] convert_to_csv
[START] [2019-12-31 10:08:37] calculate_delta
[CMD] [2019-12-31 10:08:37] echo "0a" > /app/public/diff/fdtdt_agents_19813.diff
[CMD] [2019-12-31 10:08:38] tail -n +1 /app/public/converted_csv/fdtdt_agents_19813.csv >> /app/public/diff/fdtdt_agents_19813.diff
[CMD] [2019-12-31 10:08:39] echo "." >> /app/public/diff/fdtdt_agents_19813.diff
[CMD] [2019-12-31 10:08:39] echo "0a" > /app/public/diff/fdtdt_nodes_19814.diff
[CMD] [2019-12-31 10:08:40] tail -n +1 /app/public/converted_csv/fdtdt_nodes_19814.csv >> /app/public/diff/fdtdt_nodes_19814.diff
[CMD] [2019-12-31 10:08:41] echo "." >> /app/public/diff/fdtdt_nodes_19814.diff
[CMD] [2019-12-31 10:08:41] echo "0a" > /app/public/diff/fdtdt_media_19815.diff
[CMD] [2019-12-31 10:08:42] tail -n +1 /app/public/converted_csv/fdtdt_media_19815.csv >> /app/public/diff/fdtdt_media_19815.diff
[CMD] [2019-12-31 10:08:42] echo "." >> /app/public/diff/fdtdt_media_19815.diff
[CMD] [2019-12-31 10:08:43] echo "0a" > /app/public/diff/fdtdt_vernaculars_19816.diff
[CMD] [2019-12-31 10:08:44] tail -n +1 /app/public/converted_csv/fdtdt_vernaculars_19816.csv >> /app/public/diff/fdtdt_vernaculars_19816.diff
[CMD] [2019-12-31 10:08:44] echo "." >> /app/public/diff/fdtdt_vernaculars_19816.diff
[STOP] [2019-12-31 10:08:45] calculate_delta
[START] [2019-12-31 10:08:45] parse_diff_and_store
[INFO] [2019-12-31 10:08:46] Loading agents diff file into memory (true lines)...
[INFO] [2019-12-31 10:08:46] Loading nodes diff file into memory (true lines)...
[INFO] [2019-12-31 10:08:48] Loading media diff file into memory (true lines)...
[INFO] [2019-12-31 10:09:05] Loading vernaculars diff file into memory (true lines)...
[INFO] [2019-12-31 10:09:06] Storing 96 Attributions
[INFO] [2019-12-31 10:09:06] Processing group of 96 in 1 groups of 1000
[INFO] [2019-12-31 10:09:06] Average Time: 0.04
[INFO] [2019-12-31 10:09:06] Total Time: 1s
[INFO] [2019-12-31 10:09:06] Storing 3294 ScientificNames
[INFO] [2019-12-31 10:09:06] Processing group of 3294 in 4 groups of 1000
[INFO] [2019-12-31 10:09:07] Average Time: 0.448
[INFO] [2019-12-31 10:09:07] Total Time: 2s
[INFO] [2019-12-31 10:09:07] Storing 3294 Nodes
[INFO] [2019-12-31 10:09:07] Processing group of 3294 in 4 groups of 1000
[INFO] [2019-12-31 10:09:09] Average Time: 0.358
[INFO] [2019-12-31 10:09:09] Total Time: 2s
[INFO] [2019-12-31 10:09:09] Storing 16664 ContentAttributions
[INFO] [2019-12-31 10:09:09] Processing group of 16664 in 17 groups of 1000
[INFO] [2019-12-31 10:09:11] Average Time: 0.133
[INFO] [2019-12-31 10:09:11] Total Time: 3s
[INFO] [2019-12-31 10:09:11] last 3 / first 3: 0.9
[INFO] [2019-12-31 10:09:11] Std.Dev: 0.03162277660168379; Max: 0.2
[INFO] [2019-12-31 10:09:11] Storing 10954 ArticlesSections
[INFO] [2019-12-31 10:09:11] Processing group of 10954 in 11 groups of 1000
[INFO] [2019-12-31 10:09:12] Average Time: 0.091
[INFO] [2019-12-31 10:09:12] Total Time: 2s
[INFO] [2019-12-31 10:09:12] last 3 / first 3: 0.88
[INFO] [2019-12-31 10:09:12] Std.Dev: 0.0; Max: 0.14
[INFO] [2019-12-31 10:09:12] Storing 10954 Articles
[INFO] [2019-12-31 10:09:12] Processing group of 10954 in 11 groups of 1000
[INFO] [2019-12-31 10:09:17] Average Time: 0.409
[INFO] [2019-12-31 10:09:17] Total Time: 5s
[INFO] [2019-12-31 10:09:17] last 3 / first 3: 0.95
[INFO] [2019-12-31 10:09:17] Std.Dev: 0.03162277660168379; Max: 0.46
[INFO] [2019-12-31 10:09:17] Storing 2800 Media
[INFO] [2019-12-31 10:09:17] Processing group of 2800 in 3 groups of 1000
[INFO] [2019-12-31 10:09:19] Average Time: 0.557
[INFO] [2019-12-31 10:09:19] Total Time: 2s
[INFO] [2019-12-31 10:09:19] Storing 2940 Vernaculars
[INFO] [2019-12-31 10:09:19] Processing group of 2940 in 3 groups of 1000
[INFO] [2019-12-31 10:09:19] Average Time: 0.277
[INFO] [2019-12-31 10:09:19] Total Time: 1s
[STOP] [2019-12-31 10:09:20] parse_diff_and_store
[START] [2019-12-31 10:09:20] resolve_keys
[INFO] [2019-12-31 10:09:34] Occurrences to nodes (through scientific_names)...
[INFO] [2019-12-31 10:09:34] traits to occurrences...
[INFO] [2019-12-31 10:09:34] traits to nodes (through occurrences)...
[INFO] [2019-12-31 10:09:34] Traits to sex term...
[INFO] [2019-12-31 10:09:34] Traits to lifestage term...
[INFO] [2019-12-31 10:09:34] MetaTraits to traits...
[INFO] [2019-12-31 10:09:34] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-12-31 10:09:34] Assocs to occurrences...
[INFO] [2019-12-31 10:09:34] Assocs to nodes...
[INFO] [2019-12-31 10:09:34] Assoc to sex term...
[INFO] [2019-12-31 10:09:34] Assoc to lifestage term...
[STOP] [2019-12-31 10:09:35] resolve_keys
[START] [2019-12-31 10:09:35] hold_for_later_1
[STOP] [2019-12-31 10:09:35] hold_for_later_1
[START] [2019-12-31 10:09:35] hold_for_later_2
[STOP] [2019-12-31 10:09:35] hold_for_later_2
[START] [2019-12-31 10:09:35] resolve_missing_parents
[STOP] [2019-12-31 10:09:35] resolve_missing_parents
[START] [2019-12-31 10:09:35] rebuild_nodes
[START] [2019-12-31 10:09:35] Flattener#flatten
[START] [2019-12-31 10:09:35] Flattener#study_resource
[START] [2019-12-31 10:09:35] Flattener#build_ancestry
[STOP] [2019-12-31 10:09:35] Flattener#build_ancestry
[INFO] [2019-12-31 10:09:35] 3294 ancestry keys
[START] [2019-12-31 10:09:35] build_node_ancestors
[INFO] [2019-12-31 10:09:35] old ancestors deleted.
[STOP] [2019-12-31 10:09:36] build_node_ancestors
[START] [2019-12-31 10:09:37] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:09:38] Flattener#propagate_ancestor_ids
[STOP] [2019-12-31 10:09:38] Flattener#flatten
[STOP] [2019-12-31 10:09:38] rebuild_nodes
[START] [2019-12-31 10:09:38] resolve_missing_media_owners
[STOP] [2019-12-31 10:09:38] resolve_missing_media_owners
[START] [2019-12-31 10:09:38] sanitize_media_verbatims
[STOP] [2019-12-31 10:09:38] sanitize_media_verbatims
[START] [2019-12-31 10:09:38] queue_downloads
[STOP] [2019-12-31 10:09:38] queue_downloads
[START] [2019-12-31 10:09:38] parse_names
[WARN] [2019-12-31 10:09:38] I see 3294 names which still need to be parsed.
[STOP] [2019-12-31 10:09:42] parse_names
[START] [2019-12-31 10:09:42] denormalize_canonical_names_to_nodes
[STOP] [2019-12-31 10:09:42] denormalize_canonical_names_to_nodes
[START] [2019-12-31 10:09:42] match_nodes
[START] [2019-12-31 10:09:42] map_all_nodes_to_pages
[ERR] [2019-12-31 10:10:32][hdls] download_and_prep FAILED for Medium.find(10375612): 404 Not Found
[ERR] [2019-12-31 10:10:32][hdls] download_and_prep FAILED for Medium.find(10375620): 404 Not Found
[ERR] [2019-12-31 10:10:35][hdls] download_and_prep FAILED for Medium.find(10375637): 404 Not Found
[ERR] [2019-12-31 10:10:40][hdls] download_and_prep FAILED for Medium.find(10375682): 404 Not Found
[ERR] [2019-12-31 10:13:20][hdls] download_and_prep FAILED for Medium.find(10376356): 404 Not Found
[STOP] [2019-12-31 10:17:23] map_all_nodes_to_pages
[INFO] [2019-12-31 10:17:23] Unmatched nodes (10 of 3294): Bathysauroidae (#62745189); Gasterosteiformes (#62742405); Macroramphosidae (#62742414); Apogon striatus (#62742708); Cepolidae (#62742922); Ptereleotridae (#62743514); Scorpaeniformes (#62744189); Caracanthidae (#62744198); Diplphidae (#62744349); Echinorhiniformes (#62744692)
[START] [2019-12-31 10:17:23] update_nodes
[STOP] [2019-12-31 10:17:24] update_nodes
[STOP] [2019-12-31 10:17:24] match_nodes
[START] [2019-12-31 10:17:25] reindex_search
[STOP] [2019-12-31 10:17:30] reindex_search
[START] [2019-12-31 10:17:30] normalize_units
[STOP] [2019-12-31 10:17:30] normalize_units
[START] [2019-12-31 10:17:30] calculate_statistics
[STOP] [2019-12-31 10:17:30] calculate_statistics
[START] [2019-12-31 10:17:30] complete_harvest_instance
[START] [2019-12-31 10:17:30] overall_tsv_creation
[INFO] [2019-12-31 10:17:30] Processing group of 3294 in 1 batches of 10000
[INFO] [2019-12-31 10:18:49] Average Time: 44.45
[INFO] [2019-12-31 10:18:49] Total Time: 1m19s
[STOP] [2019-12-31 10:18:49] overall_tsv_creation
[INFO] [2019-12-31 10:18:49] Done. Check your files:
[INFO] [2019-12-31 10:18:49] (3294 lines) /app/public/data/fdtdt/publish_nodes.tsv
[INFO] [2019-12-31 10:18:50] (9493 lines) /app/public/data/fdtdt/publish_node_ancestors.tsv
[INFO] [2019-12-31 10:18:51] (3294 lines) /app/public/data/fdtdt/publish_scientific_names.tsv
[INFO] [2019-12-31 10:18:51] (2800 lines) /app/public/data/fdtdt/publish_media.tsv
[INFO] [2019-12-31 10:18:52] (10954 lines) /app/public/data/fdtdt/publish_articles.tsv
[INFO] [2019-12-31 10:18:53] (1787 lines) /app/public/data/fdtdt/publish_image_info.tsv
[INFO] [2019-12-31 10:18:54] (2940 lines) /app/public/data/fdtdt/publish_vernaculars.tsv
[INFO] [2019-12-31 10:18:54] (16664 lines) /app/public/data/fdtdt/publish_attributions.tsv
[INFO] [2019-12-31 10:18:55] (10954 lines) /app/public/data/fdtdt/publish_content_sections.tsv
[STOP] [2019-12-31 10:18:55] complete_harvest_instance
[START] [2019-12-31 10:18:55] completed
[STOP] [2019-12-31 10:18:55] completed
[STOP] [2019-12-31 10:18:55] logged process, took 622.92
[ERR] [2019-12-31 10:21:19][hdls] download_and_prep FAILED for Medium.find(10377938): 404 Not Found
[ERR] [2019-12-31 10:21:36][hdls] download_and_prep FAILED for Medium.find(10378023): 404 Not Found
[ERR] [2019-12-31 10:21:36][hdls] download_and_prep FAILED for Medium.find(10378024): 404 Not Found
[ERR] [2019-12-31 10:21:37][hdls] download_and_prep FAILED for Medium.find(10378025): 404 Not Found
[ERR] [2019-12-31 10:21:37][hdls] download_and_prep FAILED for Medium.find(10378027): 404 Not Found
[ERR] [2019-12-31 10:21:40][hdls] download_and_prep FAILED for Medium.find(10378041): 404 Not Found

Latest Process

31 Dec 10:08 EXITED currently processing 0