Harvest for Syria Species List Created 16 Oct 10:16

Stage: completed
Fetched: 16 Oct 10:16
Validated: 16 Oct 10:16
Deltas Created 16 Oct 10:16
Units Normalized: 16 Oct 10:23
Ancestry Built: 16 Oct 10:17
Nodes Matched: 16 Oct 10:23
Names Parsed: 16 Oct 10:17
New Models Stored: 16 Oct 10:16
Indexed: 16 Oct 10:23
Completed: 16 Oct 10:25
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-16 10:16:22 -0400 by logger.rb/56815
[START] [2019-10-16 10:16:22] logged process
[START] [2019-10-16 10:16:22] create_harvest_instance
[STOP] [2019-10-16 10:16:23] create_harvest_instance
[START] [2019-10-16 10:16:23] fetch_files
[STOP] [2019-10-16 10:16:23] fetch_files
[START] [2019-10-16 10:16:23] validate_each_file
[STOP] [2019-10-16 10:16:23] validate_each_file
[START] [2019-10-16 10:16:23] convert_to_csv
[CMD] [2019-10-16 10:16:23] /usr/bin/sort /app/public/converted_csv/syria_sp_list_refs_17377.csv > /app/public/converted_csv/syria_sp_list_refs_17377.csv_sorted
[CMD] [2019-10-16 10:16:24] /usr/bin/sort /app/public/converted_csv/syria_sp_list_nodes_17378.csv > /app/public/converted_csv/syria_sp_list_nodes_17378.csv_sorted
[CMD] [2019-10-16 10:16:24] /usr/bin/sort /app/public/converted_csv/syria_sp_list_occurrences_17379.csv > /app/public/converted_csv/syria_sp_list_occurrences_17379.csv_sorted
[CMD] [2019-10-16 10:16:24] /usr/bin/sort /app/public/converted_csv/syria_sp_list_measurements_17380.csv > /app/public/converted_csv/syria_sp_list_measurements_17380.csv_sorted
[STOP] [2019-10-16 10:16:24] convert_to_csv
[START] [2019-10-16 10:16:24] calculate_delta
[CMD] [2019-10-16 10:16:24] echo "0a" > /app/public/diff/syria_sp_list_refs_17377.diff
[CMD] [2019-10-16 10:16:25] tail -n +1 /app/public/converted_csv/syria_sp_list_refs_17377.csv >> /app/public/diff/syria_sp_list_refs_17377.diff
[CMD] [2019-10-16 10:16:25] echo "." >> /app/public/diff/syria_sp_list_refs_17377.diff
[CMD] [2019-10-16 10:16:25] echo "0a" > /app/public/diff/syria_sp_list_nodes_17378.diff
[CMD] [2019-10-16 10:16:26] tail -n +1 /app/public/converted_csv/syria_sp_list_nodes_17378.csv >> /app/public/diff/syria_sp_list_nodes_17378.diff
[CMD] [2019-10-16 10:16:26] echo "." >> /app/public/diff/syria_sp_list_nodes_17378.diff
[CMD] [2019-10-16 10:16:26] echo "0a" > /app/public/diff/syria_sp_list_occurrences_17379.diff
[CMD] [2019-10-16 10:16:26] tail -n +1 /app/public/converted_csv/syria_sp_list_occurrences_17379.csv >> /app/public/diff/syria_sp_list_occurrences_17379.diff
[CMD] [2019-10-16 10:16:27] echo "." >> /app/public/diff/syria_sp_list_occurrences_17379.diff
[CMD] [2019-10-16 10:16:27] echo "0a" > /app/public/diff/syria_sp_list_measurements_17380.diff
[CMD] [2019-10-16 10:16:27] tail -n +1 /app/public/converted_csv/syria_sp_list_measurements_17380.csv >> /app/public/diff/syria_sp_list_measurements_17380.diff
[CMD] [2019-10-16 10:16:28] echo "." >> /app/public/diff/syria_sp_list_measurements_17380.diff
[STOP] [2019-10-16 10:16:28] calculate_delta
[START] [2019-10-16 10:16:28] parse_diff_and_store
[INFO] [2019-10-16 10:16:28] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-16 10:16:28] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-16 10:16:30] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-16 10:16:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-16 10:16:44] Storing 2 References
[INFO] [2019-10-16 10:16:44] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-16 10:16:44] Average Time: 0.0
[INFO] [2019-10-16 10:16:44] Total Time: 1s
[INFO] [2019-10-16 10:16:44] Storing 3757 ScientificNames
[INFO] [2019-10-16 10:16:44] Processing group of 3757 in 4 groups of 1000
[INFO] [2019-10-16 10:16:46] Average Time: 0.365
[INFO] [2019-10-16 10:16:46] Total Time: 2s
[INFO] [2019-10-16 10:16:46] Storing 3757 Nodes
[INFO] [2019-10-16 10:16:46] Processing group of 3757 in 4 groups of 1000
[INFO] [2019-10-16 10:16:47] Average Time: 0.277
[INFO] [2019-10-16 10:16:47] Total Time: 2s
[INFO] [2019-10-16 10:16:47] Storing 2292 Occurrences
[INFO] [2019-10-16 10:16:47] Processing group of 2292 in 3 groups of 1000
[INFO] [2019-10-16 10:16:47] Average Time: 0.08
[INFO] [2019-10-16 10:16:47] Total Time: 1s
[INFO] [2019-10-16 10:16:47] Storing 4584 TraitsReferences
[INFO] [2019-10-16 10:16:47] Processing group of 4584 in 5 groups of 1000
[INFO] [2019-10-16 10:16:48] Average Time: 0.072
[INFO] [2019-10-16 10:16:48] Total Time: 1s
[INFO] [2019-10-16 10:16:48] Storing 4584 Traits
[INFO] [2019-10-16 10:16:48] Processing group of 4584 in 5 groups of 1000
[INFO] [2019-10-16 10:16:50] Average Time: 0.348
[INFO] [2019-10-16 10:16:50] Total Time: 2s
[INFO] [2019-10-16 10:16:50] Storing 4583 MetaTraits
[INFO] [2019-10-16 10:16:50] Processing group of 4583 in 5 groups of 1000
[INFO] [2019-10-16 10:16:50] Average Time: 0.13
[INFO] [2019-10-16 10:16:50] Total Time: 1s
[STOP] [2019-10-16 10:16:50] parse_diff_and_store
[START] [2019-10-16 10:16:50] resolve_keys
[INFO] [2019-10-16 10:17:08] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-16 10:17:09] traits to occurrences...
[INFO] [2019-10-16 10:17:11] traits to nodes (through occurrences)...
[INFO] [2019-10-16 10:17:12] Traits to sex term...
[INFO] [2019-10-16 10:17:13] Traits to lifestage term...
[INFO] [2019-10-16 10:17:15] MetaTraits to traits...
[INFO] [2019-10-16 10:17:15] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-16 10:17:16] Assocs to occurrences...
[INFO] [2019-10-16 10:17:16] Assocs to nodes...
[INFO] [2019-10-16 10:17:16] Assoc to sex term...
[INFO] [2019-10-16 10:17:16] Assoc to lifestage term...
[STOP] [2019-10-16 10:17:16] resolve_keys
[START] [2019-10-16 10:17:16] hold_for_later_1
[STOP] [2019-10-16 10:17:16] hold_for_later_1
[START] [2019-10-16 10:17:16] hold_for_later_2
[STOP] [2019-10-16 10:17:16] hold_for_later_2
[START] [2019-10-16 10:17:16] resolve_missing_parents
[STOP] [2019-10-16 10:17:23] resolve_missing_parents
[START] [2019-10-16 10:17:23] rebuild_nodes
[START] [2019-10-16 10:17:23] Flattener#flatten
[START] [2019-10-16 10:17:23] Flattener#study_resource
[START] [2019-10-16 10:17:23] Flattener#build_ancestry
[STOP] [2019-10-16 10:17:25] Flattener#build_ancestry
[INFO] [2019-10-16 10:17:25] 3757 ancestry keys
[START] [2019-10-16 10:17:25] build_node_ancestors
[INFO] [2019-10-16 10:17:25] old ancestors deleted.
[STOP] [2019-10-16 10:17:27] build_node_ancestors
[START] [2019-10-16 10:17:28] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 10:17:29] Flattener#propagate_ancestor_ids
[STOP] [2019-10-16 10:17:29] Flattener#flatten
[STOP] [2019-10-16 10:17:29] rebuild_nodes
[START] [2019-10-16 10:17:29] resolve_missing_media_owners
[STOP] [2019-10-16 10:17:29] resolve_missing_media_owners
[START] [2019-10-16 10:17:29] sanitize_media_verbatims
[STOP] [2019-10-16 10:17:29] sanitize_media_verbatims
[START] [2019-10-16 10:17:29] queue_downloads
[STOP] [2019-10-16 10:17:29] queue_downloads
[START] [2019-10-16 10:17:29] parse_names
[WARN] [2019-10-16 10:17:29] I see 3757 names which still need to be parsed.
[STOP] [2019-10-16 10:17:33] parse_names
[START] [2019-10-16 10:17:33] denormalize_canonical_names_to_nodes
[STOP] [2019-10-16 10:17:33] denormalize_canonical_names_to_nodes
[START] [2019-10-16 10:17:33] match_nodes
[START] [2019-10-16 10:17:33] map_all_nodes_to_pages
[STOP] [2019-10-16 10:23:12] map_all_nodes_to_pages
[INFO] [2019-10-16 10:23:12] 205 Unmatched nodes (of 3757)! That's too many to output. First 10: Magnoliophyta (#52306440); Aegilops triaristata (#52308878); Bromus fasciculata (#52309653); Bromus sipylea (#52310044); Bromus rigida (#52310132); Phalaris tuberosa (#52306909); Elymus libanoticum (#52307061); Oryzopsis blancheanum (#52307089); Oryzopsis miliaceum (#52309968); Stipa parviflora (#52308185)
[START] [2019-10-16 10:23:12] update_nodes
[STOP] [2019-10-16 10:23:13] update_nodes
[STOP] [2019-10-16 10:23:13] match_nodes
[START] [2019-10-16 10:23:13] reindex_search
[STOP] [2019-10-16 10:23:25] reindex_search
[START] [2019-10-16 10:23:25] normalize_units
[STOP] [2019-10-16 10:23:25] normalize_units
[START] [2019-10-16 10:23:25] calculate_statistics
[STOP] [2019-10-16 10:23:25] calculate_statistics
[START] [2019-10-16 10:23:25] complete_harvest_instance
[START] [2019-10-16 10:23:25] overall_tsv_creation
[INFO] [2019-10-16 10:23:26] Processing group of 3757 in 1 batches of 10000
[INFO] [2019-10-16 10:24:26] 2292 Traits (unfiltered)...
[INFO] [2019-10-16 10:24:39] 2292 Traits (filtered)...
[INFO] [2019-10-16 10:24:39] 0 Associations (filtered)...
[INFO] [2019-10-16 10:25:20] 11459 metadata added.
[INFO] [2019-10-16 10:25:20] 0 metadata added.
[INFO] [2019-10-16 10:25:20] Average Time: 91.86
[INFO] [2019-10-16 10:25:20] Total Time: 1m55s
[STOP] [2019-10-16 10:25:20] overall_tsv_creation
[INFO] [2019-10-16 10:25:20] Done. Check your files:
[INFO] [2019-10-16 10:25:21] (3757 lines) /app/public/data/syria_sp_list/publish_nodes.tsv
[INFO] [2019-10-16 10:25:21] (20315 lines) /app/public/data/syria_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-16 10:25:21] (3757 lines) /app/public/data/syria_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-16 10:25:22] (2293 lines) /app/public/data/syria_sp_list/publish_traits.tsv
[INFO] [2019-10-16 10:25:22] (11460 lines) /app/public/data/syria_sp_list/publish_metadata.tsv
[STOP] [2019-10-16 10:25:22] complete_harvest_instance
[START] [2019-10-16 10:25:22] completed
[STOP] [2019-10-16 10:25:22] completed
[STOP] [2019-10-16 10:25:22] logged process, took 539.91
Latest Process

16 Oct 10:16 EXITED currently processing 0