Harvest for Grenada Species List Created 13 Oct 05:54

Stage: completed
Fetched: 13 Oct 05:54
Validated: 13 Oct 05:54
Deltas Created 13 Oct 05:54
Units Normalized: 13 Oct 05:56
Ancestry Built: 13 Oct 05:54
Nodes Matched: 13 Oct 05:56
Names Parsed: 13 Oct 05:54
New Models Stored: 13 Oct 05:54
Indexed: 13 Oct 05:56
Completed: 13 Oct 05:58
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-13 05:54:34 -0400 by logger.rb/56815
[START] [2019-10-13 05:54:34] logged process
[START] [2019-10-13 05:54:34] create_harvest_instance
[STOP] [2019-10-13 05:54:34] create_harvest_instance
[START] [2019-10-13 05:54:34] fetch_files
[STOP] [2019-10-13 05:54:34] fetch_files
[START] [2019-10-13 05:54:34] validate_each_file
[STOP] [2019-10-13 05:54:34] validate_each_file
[START] [2019-10-13 05:54:34] convert_to_csv
[CMD] [2019-10-13 05:54:34] /usr/bin/sort /app/public/converted_csv/grenada_sp_list2_refs_15891.csv > /app/public/converted_csv/grenada_sp_list2_refs_15891.csv_sorted
[CMD] [2019-10-13 05:54:34] /usr/bin/sort /app/public/converted_csv/grenada_sp_list2_nodes_15892.csv > /app/public/converted_csv/grenada_sp_list2_nodes_15892.csv_sorted
[CMD] [2019-10-13 05:54:35] /usr/bin/sort /app/public/converted_csv/grenada_sp_list2_occurrences_15893.csv > /app/public/converted_csv/grenada_sp_list2_occurrences_15893.csv_sorted
[CMD] [2019-10-13 05:54:35] /usr/bin/sort /app/public/converted_csv/grenada_sp_list2_measurements_15894.csv > /app/public/converted_csv/grenada_sp_list2_measurements_15894.csv_sorted
[STOP] [2019-10-13 05:54:35] convert_to_csv
[START] [2019-10-13 05:54:35] calculate_delta
[CMD] [2019-10-13 05:54:35] echo "0a" > /app/public/diff/grenada_sp_list2_refs_15891.diff
[CMD] [2019-10-13 05:54:35] tail -n +1 /app/public/converted_csv/grenada_sp_list2_refs_15891.csv >> /app/public/diff/grenada_sp_list2_refs_15891.diff
[CMD] [2019-10-13 05:54:35] echo "." >> /app/public/diff/grenada_sp_list2_refs_15891.diff
[CMD] [2019-10-13 05:54:35] echo "0a" > /app/public/diff/grenada_sp_list2_nodes_15892.diff
[CMD] [2019-10-13 05:54:35] tail -n +1 /app/public/converted_csv/grenada_sp_list2_nodes_15892.csv >> /app/public/diff/grenada_sp_list2_nodes_15892.diff
[CMD] [2019-10-13 05:54:35] echo "." >> /app/public/diff/grenada_sp_list2_nodes_15892.diff
[CMD] [2019-10-13 05:54:35] echo "0a" > /app/public/diff/grenada_sp_list2_occurrences_15893.diff
[CMD] [2019-10-13 05:54:35] tail -n +1 /app/public/converted_csv/grenada_sp_list2_occurrences_15893.csv >> /app/public/diff/grenada_sp_list2_occurrences_15893.diff
[CMD] [2019-10-13 05:54:35] echo "." >> /app/public/diff/grenada_sp_list2_occurrences_15893.diff
[CMD] [2019-10-13 05:54:36] echo "0a" > /app/public/diff/grenada_sp_list2_measurements_15894.diff
[CMD] [2019-10-13 05:54:36] tail -n +1 /app/public/converted_csv/grenada_sp_list2_measurements_15894.csv >> /app/public/diff/grenada_sp_list2_measurements_15894.diff
[CMD] [2019-10-13 05:54:36] echo "." >> /app/public/diff/grenada_sp_list2_measurements_15894.diff
[STOP] [2019-10-13 05:54:36] calculate_delta
[START] [2019-10-13 05:54:36] parse_diff_and_store
[INFO] [2019-10-13 05:54:36] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-13 05:54:36] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-13 05:54:37] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-13 05:54:37] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-13 05:54:40] Storing 2 References
[INFO] [2019-10-13 05:54:40] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-13 05:54:40] Average Time: 0.0
[INFO] [2019-10-13 05:54:40] Total Time: 1s
[INFO] [2019-10-13 05:54:40] Storing 1361 ScientificNames
[INFO] [2019-10-13 05:54:40] Processing group of 1361 in 2 groups of 1000
[INFO] [2019-10-13 05:54:41] Average Time: 0.275
[INFO] [2019-10-13 05:54:41] Total Time: 1s
[INFO] [2019-10-13 05:54:41] Storing 1361 Nodes
[INFO] [2019-10-13 05:54:41] Processing group of 1361 in 2 groups of 1000
[INFO] [2019-10-13 05:54:41] Average Time: 0.2
[INFO] [2019-10-13 05:54:41] Total Time: 1s
[INFO] [2019-10-13 05:54:41] Storing 482 Occurrences
[INFO] [2019-10-13 05:54:41] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-13 05:54:41] Average Time: 0.07
[INFO] [2019-10-13 05:54:41] Total Time: 1s
[INFO] [2019-10-13 05:54:41] Storing 1116 TraitsReferences
[INFO] [2019-10-13 05:54:41] Processing group of 1116 in 2 groups of 1000
[INFO] [2019-10-13 05:54:41] Average Time: 0.08
[INFO] [2019-10-13 05:54:41] Total Time: 1s
[INFO] [2019-10-13 05:54:41] Storing 1115 Traits
[INFO] [2019-10-13 05:54:41] Processing group of 1115 in 2 groups of 1000
[INFO] [2019-10-13 05:54:42] Average Time: 0.235
[INFO] [2019-10-13 05:54:42] Total Time: 1s
[INFO] [2019-10-13 05:54:42] Storing 1116 MetaTraits
[INFO] [2019-10-13 05:54:42] Processing group of 1116 in 2 groups of 1000
[INFO] [2019-10-13 05:54:42] Average Time: 0.095
[INFO] [2019-10-13 05:54:42] Total Time: 1s
[STOP] [2019-10-13 05:54:42] parse_diff_and_store
[START] [2019-10-13 05:54:42] resolve_keys
[INFO] [2019-10-13 05:54:49] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-13 05:54:50] traits to occurrences...
[INFO] [2019-10-13 05:54:50] traits to nodes (through occurrences)...
[INFO] [2019-10-13 05:54:50] Traits to sex term...
[INFO] [2019-10-13 05:54:50] Traits to lifestage term...
[INFO] [2019-10-13 05:54:50] MetaTraits to traits...
[INFO] [2019-10-13 05:54:50] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-13 05:54:50] Assocs to occurrences...
[INFO] [2019-10-13 05:54:50] Assocs to nodes...
[INFO] [2019-10-13 05:54:50] Assoc to sex term...
[INFO] [2019-10-13 05:54:50] Assoc to lifestage term...
[STOP] [2019-10-13 05:54:50] resolve_keys
[START] [2019-10-13 05:54:50] hold_for_later_1
[STOP] [2019-10-13 05:54:50] hold_for_later_1
[START] [2019-10-13 05:54:50] hold_for_later_2
[STOP] [2019-10-13 05:54:50] hold_for_later_2
[START] [2019-10-13 05:54:50] resolve_missing_parents
[STOP] [2019-10-13 05:54:51] resolve_missing_parents
[START] [2019-10-13 05:54:51] rebuild_nodes
[START] [2019-10-13 05:54:51] Flattener#flatten
[START] [2019-10-13 05:54:51] Flattener#study_resource
[START] [2019-10-13 05:54:51] Flattener#build_ancestry
[STOP] [2019-10-13 05:54:51] Flattener#build_ancestry
[INFO] [2019-10-13 05:54:51] 1361 ancestry keys
[START] [2019-10-13 05:54:51] build_node_ancestors
[INFO] [2019-10-13 05:54:51] old ancestors deleted.
[STOP] [2019-10-13 05:54:52] build_node_ancestors
[START] [2019-10-13 05:54:52] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 05:54:52] Flattener#propagate_ancestor_ids
[STOP] [2019-10-13 05:54:52] Flattener#flatten
[STOP] [2019-10-13 05:54:52] rebuild_nodes
[START] [2019-10-13 05:54:52] resolve_missing_media_owners
[STOP] [2019-10-13 05:54:52] resolve_missing_media_owners
[START] [2019-10-13 05:54:52] sanitize_media_verbatims
[STOP] [2019-10-13 05:54:52] sanitize_media_verbatims
[START] [2019-10-13 05:54:52] queue_downloads
[STOP] [2019-10-13 05:54:52] queue_downloads
[START] [2019-10-13 05:54:52] parse_names
[WARN] [2019-10-13 05:54:52] I see 1361 names which still need to be parsed.
[STOP] [2019-10-13 05:54:54] parse_names
[START] [2019-10-13 05:54:54] denormalize_canonical_names_to_nodes
[STOP] [2019-10-13 05:54:54] denormalize_canonical_names_to_nodes
[START] [2019-10-13 05:54:54] match_nodes
[START] [2019-10-13 05:54:54] map_all_nodes_to_pages
[STOP] [2019-10-13 05:56:16] map_all_nodes_to_pages
[INFO] [2019-10-13 05:56:16] 76 Unmatched nodes (of 1361)! That's too many to output. First 10: Coerebidae (#49937798); Limnodromus (#49937932); Thalaseus (#49937971); Thalaseus maximus (#49937970); Fulica caribaea (#49937957); Anas discors (#49937990); Anas americana (#49938422); Cardiocondyla minutior (#49938205); Strumigenys emmae (#49938332); Dermanura glaucus (#49938867)
[START] [2019-10-13 05:56:16] update_nodes
[STOP] [2019-10-13 05:56:17] update_nodes
[STOP] [2019-10-13 05:56:17] match_nodes
[START] [2019-10-13 05:56:17] reindex_search
[STOP] [2019-10-13 05:56:20] reindex_search
[START] [2019-10-13 05:56:20] normalize_units
[STOP] [2019-10-13 05:56:20] normalize_units
[START] [2019-10-13 05:56:20] calculate_statistics
[STOP] [2019-10-13 05:56:20] calculate_statistics
[START] [2019-10-13 05:56:20] complete_harvest_instance
[START] [2019-10-13 05:56:20] overall_tsv_creation
[INFO] [2019-10-13 05:56:20] Processing group of 1361 in 1 batches of 10000
[INFO] [2019-10-13 05:57:11] 482 Traits (unfiltered)...
[INFO] [2019-10-13 05:57:25] 482 Traits (filtered)...
[INFO] [2019-10-13 05:57:25] 0 Associations (filtered)...
[INFO] [2019-10-13 05:58:04] 2410 metadata added.
[INFO] [2019-10-13 05:58:04] 0 metadata added.
[INFO] [2019-10-13 05:58:04] Average Time: 82.56
[INFO] [2019-10-13 05:58:04] Total Time: 1m45s
[STOP] [2019-10-13 05:58:04] overall_tsv_creation
[INFO] [2019-10-13 05:58:04] Done. Check your files:
[INFO] [2019-10-13 05:58:04] (1361 lines) /app/public/data/grenada_sp_list2/publish_nodes.tsv
[INFO] [2019-10-13 05:58:04] (4001 lines) /app/public/data/grenada_sp_list2/publish_node_ancestors.tsv
[INFO] [2019-10-13 05:58:04] (1361 lines) /app/public/data/grenada_sp_list2/publish_scientific_names.tsv
[INFO] [2019-10-13 05:58:04] (483 lines) /app/public/data/grenada_sp_list2/publish_traits.tsv
[INFO] [2019-10-13 05:58:05] (2411 lines) /app/public/data/grenada_sp_list2/publish_metadata.tsv
[STOP] [2019-10-13 05:58:05] complete_harvest_instance
[START] [2019-10-13 05:58:05] completed
[STOP] [2019-10-13 05:58:05] completed
[STOP] [2019-10-13 05:58:05] logged process, took 210.93
Latest Process

13 Oct 05:54 EXITED currently processing 0