Harvest for Qatar Species List Created 15 Oct 13:50

Stage: completed
Fetched: 15 Oct 13:50
Validated: 15 Oct 13:50
Deltas Created 15 Oct 13:50
Units Normalized: 15 Oct 13:52
Ancestry Built: 15 Oct 13:51
Nodes Matched: 15 Oct 13:52
Names Parsed: 15 Oct 13:51
New Models Stored: 15 Oct 13:51
Indexed: 15 Oct 13:52
Completed: 15 Oct 13:54
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-15 13:50:51 -0400 by logger.rb/56815
[START] [2019-10-15 13:50:51] logged process
[START] [2019-10-15 13:50:51] create_harvest_instance
[STOP] [2019-10-15 13:50:51] create_harvest_instance
[START] [2019-10-15 13:50:51] fetch_files
[STOP] [2019-10-15 13:50:51] fetch_files
[START] [2019-10-15 13:50:51] validate_each_file
[STOP] [2019-10-15 13:50:52] validate_each_file
[START] [2019-10-15 13:50:52] convert_to_csv
[CMD] [2019-10-15 13:50:52] /usr/bin/sort /app/public/converted_csv/qatar_sp_list_refs_16957.csv > /app/public/converted_csv/qatar_sp_list_refs_16957.csv_sorted
[CMD] [2019-10-15 13:50:52] /usr/bin/sort /app/public/converted_csv/qatar_sp_list_nodes_16958.csv > /app/public/converted_csv/qatar_sp_list_nodes_16958.csv_sorted
[CMD] [2019-10-15 13:50:52] /usr/bin/sort /app/public/converted_csv/qatar_sp_list_occurrences_16959.csv > /app/public/converted_csv/qatar_sp_list_occurrences_16959.csv_sorted
[CMD] [2019-10-15 13:50:52] /usr/bin/sort /app/public/converted_csv/qatar_sp_list_measurements_16960.csv > /app/public/converted_csv/qatar_sp_list_measurements_16960.csv_sorted
[STOP] [2019-10-15 13:50:53] convert_to_csv
[START] [2019-10-15 13:50:53] calculate_delta
[CMD] [2019-10-15 13:50:53] echo "0a" > /app/public/diff/qatar_sp_list_refs_16957.diff
[CMD] [2019-10-15 13:50:53] tail -n +1 /app/public/converted_csv/qatar_sp_list_refs_16957.csv >> /app/public/diff/qatar_sp_list_refs_16957.diff
[CMD] [2019-10-15 13:50:53] echo "." >> /app/public/diff/qatar_sp_list_refs_16957.diff
[CMD] [2019-10-15 13:50:53] echo "0a" > /app/public/diff/qatar_sp_list_nodes_16958.diff
[CMD] [2019-10-15 13:50:54] tail -n +1 /app/public/converted_csv/qatar_sp_list_nodes_16958.csv >> /app/public/diff/qatar_sp_list_nodes_16958.diff
[CMD] [2019-10-15 13:50:54] echo "." >> /app/public/diff/qatar_sp_list_nodes_16958.diff
[CMD] [2019-10-15 13:50:54] echo "0a" > /app/public/diff/qatar_sp_list_occurrences_16959.diff
[CMD] [2019-10-15 13:50:55] tail -n +1 /app/public/converted_csv/qatar_sp_list_occurrences_16959.csv >> /app/public/diff/qatar_sp_list_occurrences_16959.diff
[CMD] [2019-10-15 13:50:55] echo "." >> /app/public/diff/qatar_sp_list_occurrences_16959.diff
[CMD] [2019-10-15 13:50:55] echo "0a" > /app/public/diff/qatar_sp_list_measurements_16960.diff
[CMD] [2019-10-15 13:50:55] tail -n +1 /app/public/converted_csv/qatar_sp_list_measurements_16960.csv >> /app/public/diff/qatar_sp_list_measurements_16960.diff
[CMD] [2019-10-15 13:50:56] echo "." >> /app/public/diff/qatar_sp_list_measurements_16960.diff
[STOP] [2019-10-15 13:50:56] calculate_delta
[START] [2019-10-15 13:50:56] parse_diff_and_store
[INFO] [2019-10-15 13:50:56] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-15 13:50:57] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-15 13:50:57] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-15 13:50:57] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-15 13:50:59] Storing 2 References
[INFO] [2019-10-15 13:50:59] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-15 13:50:59] Average Time: 0.0
[INFO] [2019-10-15 13:50:59] Total Time: 1s
[INFO] [2019-10-15 13:50:59] Storing 744 ScientificNames
[INFO] [2019-10-15 13:50:59] Processing group of 744 in 1 groups of 1000
[INFO] [2019-10-15 13:51:00] Average Time: 0.36
[INFO] [2019-10-15 13:51:00] Total Time: 1s
[INFO] [2019-10-15 13:51:00] Storing 744 Nodes
[INFO] [2019-10-15 13:51:00] Processing group of 744 in 1 groups of 1000
[INFO] [2019-10-15 13:51:00] Average Time: 0.24
[INFO] [2019-10-15 13:51:00] Total Time: 1s
[INFO] [2019-10-15 13:51:00] Storing 328 Occurrences
[INFO] [2019-10-15 13:51:00] Processing group of 328 in 1 groups of 1000
[INFO] [2019-10-15 13:51:00] Average Time: 0.06
[INFO] [2019-10-15 13:51:00] Total Time: 1s
[INFO] [2019-10-15 13:51:00] Storing 656 TraitsReferences
[INFO] [2019-10-15 13:51:00] Processing group of 656 in 1 groups of 1000
[INFO] [2019-10-15 13:51:00] Average Time: 0.13
[INFO] [2019-10-15 13:51:00] Total Time: 1s
[INFO] [2019-10-15 13:51:00] Storing 656 Traits
[INFO] [2019-10-15 13:51:00] Processing group of 656 in 1 groups of 1000
[INFO] [2019-10-15 13:51:00] Average Time: 0.29
[INFO] [2019-10-15 13:51:00] Total Time: 1s
[INFO] [2019-10-15 13:51:00] Storing 656 MetaTraits
[INFO] [2019-10-15 13:51:00] Processing group of 656 in 1 groups of 1000
[INFO] [2019-10-15 13:51:01] Average Time: 0.11
[INFO] [2019-10-15 13:51:01] Total Time: 1s
[STOP] [2019-10-15 13:51:01] parse_diff_and_store
[START] [2019-10-15 13:51:01] resolve_keys
[INFO] [2019-10-15 13:51:06] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-15 13:51:06] traits to occurrences...
[INFO] [2019-10-15 13:51:06] traits to nodes (through occurrences)...
[INFO] [2019-10-15 13:51:06] Traits to sex term...
[INFO] [2019-10-15 13:51:06] Traits to lifestage term...
[INFO] [2019-10-15 13:51:06] MetaTraits to traits...
[INFO] [2019-10-15 13:51:06] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-15 13:51:06] Assocs to occurrences...
[INFO] [2019-10-15 13:51:06] Assocs to nodes...
[INFO] [2019-10-15 13:51:06] Assoc to sex term...
[INFO] [2019-10-15 13:51:06] Assoc to lifestage term...
[STOP] [2019-10-15 13:51:06] resolve_keys
[START] [2019-10-15 13:51:06] hold_for_later_1
[STOP] [2019-10-15 13:51:06] hold_for_later_1
[START] [2019-10-15 13:51:06] hold_for_later_2
[STOP] [2019-10-15 13:51:06] hold_for_later_2
[START] [2019-10-15 13:51:06] resolve_missing_parents
[STOP] [2019-10-15 13:51:07] resolve_missing_parents
[START] [2019-10-15 13:51:07] rebuild_nodes
[START] [2019-10-15 13:51:07] Flattener#flatten
[START] [2019-10-15 13:51:07] Flattener#study_resource
[START] [2019-10-15 13:51:07] Flattener#build_ancestry
[STOP] [2019-10-15 13:51:07] Flattener#build_ancestry
[INFO] [2019-10-15 13:51:07] 744 ancestry keys
[START] [2019-10-15 13:51:07] build_node_ancestors
[INFO] [2019-10-15 13:51:07] old ancestors deleted.
[STOP] [2019-10-15 13:51:07] build_node_ancestors
[START] [2019-10-15 13:51:07] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 13:51:07] Flattener#propagate_ancestor_ids
[STOP] [2019-10-15 13:51:07] Flattener#flatten
[STOP] [2019-10-15 13:51:07] rebuild_nodes
[START] [2019-10-15 13:51:07] resolve_missing_media_owners
[STOP] [2019-10-15 13:51:07] resolve_missing_media_owners
[START] [2019-10-15 13:51:07] sanitize_media_verbatims
[STOP] [2019-10-15 13:51:07] sanitize_media_verbatims
[START] [2019-10-15 13:51:07] queue_downloads
[STOP] [2019-10-15 13:51:07] queue_downloads
[START] [2019-10-15 13:51:07] parse_names
[WARN] [2019-10-15 13:51:07] I see 744 names which still need to be parsed.
[STOP] [2019-10-15 13:51:09] parse_names
[START] [2019-10-15 13:51:09] denormalize_canonical_names_to_nodes
[STOP] [2019-10-15 13:51:09] denormalize_canonical_names_to_nodes
[START] [2019-10-15 13:51:09] match_nodes
[START] [2019-10-15 13:51:09] map_all_nodes_to_pages
[STOP] [2019-10-15 13:52:32] map_all_nodes_to_pages
[INFO] [2019-10-15 13:52:32] 36 Unmatched nodes (of 744)! That's too many to output. First 10: Erythropygia (#51683424); Erythropygia galactotes (#51683423); Calandrella rufescens (#51683522); Hypocolidae (#51683577); Streptopelia senegalensis (#51683181); Philomachus (#51683401); Philomachus pugnax (#51683400); Limicola (#51683541); Limicola falcinellus (#51683540); Thalaseus (#51683446)
[START] [2019-10-15 13:52:32] update_nodes
[STOP] [2019-10-15 13:52:33] update_nodes
[STOP] [2019-10-15 13:52:33] match_nodes
[START] [2019-10-15 13:52:33] reindex_search
[STOP] [2019-10-15 13:52:35] reindex_search
[START] [2019-10-15 13:52:35] normalize_units
[STOP] [2019-10-15 13:52:35] normalize_units
[START] [2019-10-15 13:52:35] calculate_statistics
[STOP] [2019-10-15 13:52:35] calculate_statistics
[START] [2019-10-15 13:52:35] complete_harvest_instance
[START] [2019-10-15 13:52:35] overall_tsv_creation
[INFO] [2019-10-15 13:52:35] Processing group of 744 in 1 batches of 10000
[INFO] [2019-10-15 13:53:23] 328 Traits (unfiltered)...
[INFO] [2019-10-15 13:53:36] 328 Traits (filtered)...
[INFO] [2019-10-15 13:53:36] 0 Associations (filtered)...
[INFO] [2019-10-15 13:54:14] 1640 metadata added.
[INFO] [2019-10-15 13:54:14] 0 metadata added.
[INFO] [2019-10-15 13:54:14] Average Time: 77.31
[INFO] [2019-10-15 13:54:14] Total Time: 1m39s
[STOP] [2019-10-15 13:54:14] overall_tsv_creation
[INFO] [2019-10-15 13:54:14] Done. Check your files:
[INFO] [2019-10-15 13:54:14] (744 lines) /app/public/data/qatar_sp_list/publish_nodes.tsv
[INFO] [2019-10-15 13:54:14] (3613 lines) /app/public/data/qatar_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-15 13:54:15] (744 lines) /app/public/data/qatar_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-15 13:54:15] (329 lines) /app/public/data/qatar_sp_list/publish_traits.tsv
[INFO] [2019-10-15 13:54:15] (1641 lines) /app/public/data/qatar_sp_list/publish_metadata.tsv
[STOP] [2019-10-15 13:54:15] complete_harvest_instance
[START] [2019-10-15 13:54:15] completed
[STOP] [2019-10-15 13:54:15] completed
[STOP] [2019-10-15 13:54:15] logged process, took 204.3
Latest Process

15 Oct 13:50 EXITED currently processing 0