Harvest for Iraq Species List Created 13 Oct 18:12

Stage: completed
Fetched: 13 Oct 18:12
Validated: 13 Oct 18:12
Deltas Created 13 Oct 18:12
Units Normalized: 13 Oct 18:15
Ancestry Built: 13 Oct 18:13
Nodes Matched: 13 Oct 18:15
Names Parsed: 13 Oct 18:13
New Models Stored: 13 Oct 18:13
Indexed: 13 Oct 18:15
Completed: 13 Oct 18:17
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-13 18:12:49 -0400 by logger.rb/56815
[START] [2019-10-13 18:12:49] logged process
[START] [2019-10-13 18:12:49] create_harvest_instance
[STOP] [2019-10-13 18:12:50] create_harvest_instance
[START] [2019-10-13 18:12:50] fetch_files
[STOP] [2019-10-13 18:12:50] fetch_files
[START] [2019-10-13 18:12:50] validate_each_file
[STOP] [2019-10-13 18:12:50] validate_each_file
[START] [2019-10-13 18:12:50] convert_to_csv
[CMD] [2019-10-13 18:12:50] /usr/bin/sort /app/public/converted_csv/iraq_sp_list_refs_16187.csv > /app/public/converted_csv/iraq_sp_list_refs_16187.csv_sorted
[CMD] [2019-10-13 18:12:50] /usr/bin/sort /app/public/converted_csv/iraq_sp_list_nodes_16188.csv > /app/public/converted_csv/iraq_sp_list_nodes_16188.csv_sorted
[CMD] [2019-10-13 18:12:51] /usr/bin/sort /app/public/converted_csv/iraq_sp_list_occurrences_16189.csv > /app/public/converted_csv/iraq_sp_list_occurrences_16189.csv_sorted
[CMD] [2019-10-13 18:12:51] /usr/bin/sort /app/public/converted_csv/iraq_sp_list_measurements_16190.csv > /app/public/converted_csv/iraq_sp_list_measurements_16190.csv_sorted
[STOP] [2019-10-13 18:12:51] convert_to_csv
[START] [2019-10-13 18:12:51] calculate_delta
[CMD] [2019-10-13 18:12:51] echo "0a" > /app/public/diff/iraq_sp_list_refs_16187.diff
[CMD] [2019-10-13 18:12:51] tail -n +1 /app/public/converted_csv/iraq_sp_list_refs_16187.csv >> /app/public/diff/iraq_sp_list_refs_16187.diff
[CMD] [2019-10-13 18:12:51] echo "." >> /app/public/diff/iraq_sp_list_refs_16187.diff
[CMD] [2019-10-13 18:12:51] echo "0a" > /app/public/diff/iraq_sp_list_nodes_16188.diff
[CMD] [2019-10-13 18:12:51] tail -n +1 /app/public/converted_csv/iraq_sp_list_nodes_16188.csv >> /app/public/diff/iraq_sp_list_nodes_16188.diff
[CMD] [2019-10-13 18:12:51] echo "." >> /app/public/diff/iraq_sp_list_nodes_16188.diff
[CMD] [2019-10-13 18:12:51] echo "0a" > /app/public/diff/iraq_sp_list_occurrences_16189.diff
[CMD] [2019-10-13 18:12:51] tail -n +1 /app/public/converted_csv/iraq_sp_list_occurrences_16189.csv >> /app/public/diff/iraq_sp_list_occurrences_16189.diff
[CMD] [2019-10-13 18:12:51] echo "." >> /app/public/diff/iraq_sp_list_occurrences_16189.diff
[CMD] [2019-10-13 18:12:52] echo "0a" > /app/public/diff/iraq_sp_list_measurements_16190.diff
[CMD] [2019-10-13 18:12:52] tail -n +1 /app/public/converted_csv/iraq_sp_list_measurements_16190.csv >> /app/public/diff/iraq_sp_list_measurements_16190.diff
[CMD] [2019-10-13 18:12:52] echo "." >> /app/public/diff/iraq_sp_list_measurements_16190.diff
[STOP] [2019-10-13 18:12:52] calculate_delta
[START] [2019-10-13 18:12:52] parse_diff_and_store
[INFO] [2019-10-13 18:12:52] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 18:12:52] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 18:12:53] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 18:12:53] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 18:13:03] Storing 2 References
[INFO] [2019-10-13 18:13:03] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 18:13:03] Average Time: 0.0
[INFO] [2019-10-13 18:13:03] Total Time: 1s
[INFO] [2019-10-13 18:13:03] Storing 2351 ScientificNames
[INFO] [2019-10-13 18:13:03] Processing group of 2351 in 3 groups of 1000
[INFO] [2019-10-13 18:13:04] Average Time: 0.303
[INFO] [2019-10-13 18:13:04] Total Time: 1s
[INFO] [2019-10-13 18:13:04] Storing 2351 Nodes
[INFO] [2019-10-13 18:13:04] Processing group of 2351 in 3 groups of 1000
[INFO] [2019-10-13 18:13:04] Average Time: 0.243
[INFO] [2019-10-13 18:13:04] Total Time: 1s
[INFO] [2019-10-13 18:13:04] Storing 964 Occurrences
[INFO] [2019-10-13 18:13:04] Processing group of 964 in 1 groups of 1000
[INFO] [2019-10-13 18:13:04] Average Time: 0.11
[INFO] [2019-10-13 18:13:04] Total Time: 1s
[INFO] [2019-10-13 18:13:04] Storing 2820 TraitsReferences
[INFO] [2019-10-13 18:13:04] Processing group of 2820 in 3 groups of 1000
[INFO] [2019-10-13 18:13:05] Average Time: 0.09
[INFO] [2019-10-13 18:13:05] Total Time: 1s
[INFO] [2019-10-13 18:13:05] Storing 2819 Traits
[INFO] [2019-10-13 18:13:05] Processing group of 2819 in 3 groups of 1000
[INFO] [2019-10-13 18:13:06] Average Time: 0.367
[INFO] [2019-10-13 18:13:06] Total Time: 2s
[INFO] [2019-10-13 18:13:06] Storing 2819 MetaTraits
[INFO] [2019-10-13 18:13:06] Processing group of 2819 in 3 groups of 1000
[INFO] [2019-10-13 18:13:06] Average Time: 0.173
[INFO] [2019-10-13 18:13:06] Total Time: 1s
[STOP] [2019-10-13 18:13:06] parse_diff_and_store
[START] [2019-10-13 18:13:06] resolve_keys
[INFO] [2019-10-13 18:13:18] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 18:13:19] traits to occurrences...
[INFO] [2019-10-13 18:13:20] traits to nodes (through occurrences)...
[INFO] [2019-10-13 18:13:20] Traits to sex term...
[INFO] [2019-10-13 18:13:21] Traits to lifestage term...
[INFO] [2019-10-13 18:13:22] MetaTraits to traits...
[INFO] [2019-10-13 18:13:22] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 18:13:22] Assocs to occurrences...
[INFO] [2019-10-13 18:13:22] Assocs to nodes...
[INFO] [2019-10-13 18:13:22] Assoc to sex term...
[INFO] [2019-10-13 18:13:22] Assoc to lifestage term...
[STOP] [2019-10-13 18:13:22] resolve_keys
[START] [2019-10-13 18:13:22] hold_for_later_1
[STOP] [2019-10-13 18:13:22] hold_for_later_1
[START] [2019-10-13 18:13:22] hold_for_later_2
[STOP] [2019-10-13 18:13:22] hold_for_later_2
[START] [2019-10-13 18:13:22] resolve_missing_parents
[STOP] [2019-10-13 18:13:26] resolve_missing_parents
[START] [2019-10-13 18:13:26] rebuild_nodes
[START] [2019-10-13 18:13:26] Flattener#flatten
[START] [2019-10-13 18:13:26] Flattener#study_resource
[START] [2019-10-13 18:13:26] Flattener#build_ancestry
[STOP] [2019-10-13 18:13:26] Flattener#build_ancestry
[INFO] [2019-10-13 18:13:26] 2351 ancestry keys
[START] [2019-10-13 18:13:26] build_node_ancestors
[INFO] [2019-10-13 18:13:26] old ancestors deleted.
[STOP] [2019-10-13 18:13:26] build_node_ancestors
[START] [2019-10-13 18:13:27] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 18:13:27] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 18:13:27] Flattener#flatten
[STOP] [2019-10-13 18:13:27] rebuild_nodes
[START] [2019-10-13 18:13:27] resolve_missing_media_owners
[STOP] [2019-10-13 18:13:27] resolve_missing_media_owners
[START] [2019-10-13 18:13:27] sanitize_media_verbatims
[STOP] [2019-10-13 18:13:27] sanitize_media_verbatims
[START] [2019-10-13 18:13:27] queue_downloads
[STOP] [2019-10-13 18:13:27] queue_downloads
[START] [2019-10-13 18:13:27] parse_names
[WARN] [2019-10-13 18:13:27] I see 2351 names which still need to be parsed.
[STOP] [2019-10-13 18:13:30] parse_names
[START] [2019-10-13 18:13:30] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 18:13:30] denormalize_canonical_names_to_nodes
[START] [2019-10-13 18:13:30] match_nodes
[START] [2019-10-13 18:13:30] map_all_nodes_to_pages
[STOP] [2019-10-13 18:15:33] map_all_nodes_to_pages
[INFO] [2019-10-13 18:15:33] 136 Unmatched nodes (of 2351)! That's too many to output. First 10: Petronia xanthocollis (#50300119); Streptopelia senegalensis (#50299510); Aegilops triaristata (#50300871); Aegilops ovatum (#50301191); Phalaris tuberosa (#50300026); Thinopyrum hispidus (#50300037); Elymus elongatum (#50301208); Elymus elongatiforme (#50301565); Cenchrus caput-medusae (#50300412); Agropyron kosaninii (#50300491)
[START] [2019-10-13 18:15:33] update_nodes
[STOP] [2019-10-13 18:15:33] update_nodes
[STOP] [2019-10-13 18:15:33] match_nodes
[START] [2019-10-13 18:15:33] reindex_search
[STOP] [2019-10-13 18:15:38] reindex_search
[START] [2019-10-13 18:15:38] normalize_units
[STOP] [2019-10-13 18:15:38] normalize_units
[START] [2019-10-13 18:15:38] calculate_statistics
[STOP] [2019-10-13 18:15:38] calculate_statistics
[START] [2019-10-13 18:15:38] complete_harvest_instance
[START] [2019-10-13 18:15:38] overall_tsv_creation
[INFO] [2019-10-13 18:15:38] Processing group of 2351 in 1 batches of 10000
[INFO] [2019-10-13 18:16:33] 964 Traits (unfiltered)...
[INFO] [2019-10-13 18:16:47] 964 Traits (filtered)...
[INFO] [2019-10-13 18:16:47] 0 Associations (filtered)...
[INFO] [2019-10-13 18:17:25] 4820 metadata added.
[INFO] [2019-10-13 18:17:25] 0 metadata added.
[INFO] [2019-10-13 18:17:26] Average Time: 85.12
[INFO] [2019-10-13 18:17:26] Total Time: 1m48s
[STOP] [2019-10-13 18:17:26] overall_tsv_creation
[INFO] [2019-10-13 18:17:26] Done. Check your files:
[INFO] [2019-10-13 18:17:26] (2351 lines) /app/public/data/iraq_sp_list/publish_nodes.tsv
[INFO] [2019-10-13 18:17:26] (3431 lines) /app/public/data/iraq_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-13 18:17:26] (2351 lines) /app/public/data/iraq_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-13 18:17:26] (965 lines) /app/public/data/iraq_sp_list/publish_traits.tsv
[INFO] [2019-10-13 18:17:26] (4821 lines) /app/public/data/iraq_sp_list/publish_metadata.tsv
[STOP] [2019-10-13 18:17:26] complete_harvest_instance
[START] [2019-10-13 18:17:26] completed
[STOP] [2019-10-13 18:17:26] completed
[STOP] [2019-10-13 18:17:26] logged process, took 276.57
Latest Process

13 Oct 18:12 EXITED currently processing 0