Harvest for Curacao Species List Created 12 Oct 12:33

Stage: completed
Fetched: 12 Oct 12:33
Validated: 12 Oct 12:33
Deltas Created 12 Oct 12:33
Units Normalized: 12 Oct 12:34
Ancestry Built: 12 Oct 12:33
Nodes Matched: 12 Oct 12:34
Names Parsed: 12 Oct 12:33
New Models Stored: 12 Oct 12:33
Indexed: 12 Oct 12:34
Completed: 12 Oct 12:36
Time to Harvest: less than a minute
Harvesting Log

(139 lines)
# Logfile created on 2019-10-12 12:33:27 -0400 by logger.rb/56815
[START] [2019-10-12 12:33:27] logged process
[START] [2019-10-12 12:33:27] create_harvest_instance
[STOP] [2019-10-12 12:33:28] create_harvest_instance
[START] [2019-10-12 12:33:28] fetch_files
[STOP] [2019-10-12 12:33:28] fetch_files
[START] [2019-10-12 12:33:28] validate_each_file
[STOP] [2019-10-12 12:33:28] validate_each_file
[START] [2019-10-12 12:33:28] convert_to_csv
[CMD] [2019-10-12 12:33:28] /usr/bin/sort /app/public/converted_csv/curacao_sp_list_refs_15547.csv > /app/public/converted_csv/curacao_sp_list_refs_15547.csv_sorted
[CMD] [2019-10-12 12:33:28] /usr/bin/sort /app/public/converted_csv/curacao_sp_list_nodes_15548.csv > /app/public/converted_csv/curacao_sp_list_nodes_15548.csv_sorted
[CMD] [2019-10-12 12:33:28] /usr/bin/sort /app/public/converted_csv/curacao_sp_list_occurrences_15549.csv > /app/public/converted_csv/curacao_sp_list_occurrences_15549.csv_sorted
[CMD] [2019-10-12 12:33:28] /usr/bin/sort /app/public/converted_csv/curacao_sp_list_measurements_15550.csv > /app/public/converted_csv/curacao_sp_list_measurements_15550.csv_sorted
[STOP] [2019-10-12 12:33:29] convert_to_csv
[START] [2019-10-12 12:33:29] calculate_delta
[CMD] [2019-10-12 12:33:29] echo "0a" > /app/public/diff/curacao_sp_list_refs_15547.diff
[CMD] [2019-10-12 12:33:29] tail -n +1 /app/public/converted_csv/curacao_sp_list_refs_15547.csv >> /app/public/diff/curacao_sp_list_refs_15547.diff
[CMD] [2019-10-12 12:33:29] echo "." >> /app/public/diff/curacao_sp_list_refs_15547.diff
[CMD] [2019-10-12 12:33:29] echo "0a" > /app/public/diff/curacao_sp_list_nodes_15548.diff
[CMD] [2019-10-12 12:33:29] tail -n +1 /app/public/converted_csv/curacao_sp_list_nodes_15548.csv >> /app/public/diff/curacao_sp_list_nodes_15548.diff
[CMD] [2019-10-12 12:33:29] echo "." >> /app/public/diff/curacao_sp_list_nodes_15548.diff
[CMD] [2019-10-12 12:33:29] echo "0a" > /app/public/diff/curacao_sp_list_occurrences_15549.diff
[CMD] [2019-10-12 12:33:29] tail -n +1 /app/public/converted_csv/curacao_sp_list_occurrences_15549.csv >> /app/public/diff/curacao_sp_list_occurrences_15549.diff
[CMD] [2019-10-12 12:33:29] echo "." >> /app/public/diff/curacao_sp_list_occurrences_15549.diff
[CMD] [2019-10-12 12:33:29] echo "0a" > /app/public/diff/curacao_sp_list_measurements_15550.diff
[CMD] [2019-10-12 12:33:30] tail -n +1 /app/public/converted_csv/curacao_sp_list_measurements_15550.csv >> /app/public/diff/curacao_sp_list_measurements_15550.diff
[CMD] [2019-10-12 12:33:30] echo "." >> /app/public/diff/curacao_sp_list_measurements_15550.diff
[STOP] [2019-10-12 12:33:30] calculate_delta
[START] [2019-10-12 12:33:30] parse_diff_and_store
[INFO] [2019-10-12 12:33:30] Loading refs diff file into memory (true lines)...
[INFO] [2019-10-12 12:33:30] Loading nodes diff file into memory (true lines)...
[INFO] [2019-10-12 12:33:31] Loading occurrences diff file into memory (true lines)...
[INFO] [2019-10-12 12:33:31] Loading measurements diff file into memory (true lines)...
[INFO] [2019-10-12 12:33:35] Storing 2 References
[INFO] [2019-10-12 12:33:35] Processing group of 2 in 1 groups of 1000
[INFO] [2019-10-12 12:33:35] Average Time: 0.0
[INFO] [2019-10-12 12:33:35] Total Time: 1s
[INFO] [2019-10-12 12:33:35] Storing 1554 ScientificNames
[INFO] [2019-10-12 12:33:35] Processing group of 1554 in 2 groups of 1000
[INFO] [2019-10-12 12:33:35] Average Time: 0.31
[INFO] [2019-10-12 12:33:35] Total Time: 1s
[INFO] [2019-10-12 12:33:35] Storing 1554 Nodes
[INFO] [2019-10-12 12:33:35] Processing group of 1554 in 2 groups of 1000
[INFO] [2019-10-12 12:33:36] Average Time: 0.235
[INFO] [2019-10-12 12:33:36] Total Time: 1s
[INFO] [2019-10-12 12:33:36] Storing 482 Occurrences
[INFO] [2019-10-12 12:33:36] Processing group of 482 in 1 groups of 1000
[INFO] [2019-10-12 12:33:36] Average Time: 0.07
[INFO] [2019-10-12 12:33:36] Total Time: 1s
[INFO] [2019-10-12 12:33:36] Storing 1428 TraitsReferences
[INFO] [2019-10-12 12:33:36] Processing group of 1428 in 2 groups of 1000
[INFO] [2019-10-12 12:33:36] Average Time: 0.095
[INFO] [2019-10-12 12:33:36] Total Time: 1s
[INFO] [2019-10-12 12:33:36] Storing 1427 Traits
[INFO] [2019-10-12 12:33:36] Processing group of 1427 in 2 groups of 1000
[INFO] [2019-10-12 12:33:37] Average Time: 0.29
[INFO] [2019-10-12 12:33:37] Total Time: 1s
[INFO] [2019-10-12 12:33:37] Storing 1428 MetaTraits
[INFO] [2019-10-12 12:33:37] Processing group of 1428 in 2 groups of 1000
[INFO] [2019-10-12 12:33:37] Average Time: 0.1
[INFO] [2019-10-12 12:33:37] Total Time: 1s
[STOP] [2019-10-12 12:33:37] parse_diff_and_store
[START] [2019-10-12 12:33:37] resolve_keys
[INFO] [2019-10-12 12:33:47] Occurrences to nodes (through scientific_names)...
[INFO] [2019-10-12 12:33:47] traits to occurrences...
[INFO] [2019-10-12 12:33:47] traits to nodes (through occurrences)...
[INFO] [2019-10-12 12:33:47] Traits to sex term...
[INFO] [2019-10-12 12:33:47] Traits to lifestage term...
[INFO] [2019-10-12 12:33:48] MetaTraits to traits...
[INFO] [2019-10-12 12:33:48] MetaTraits (simple, measurement row refers to parent) to traits...
[INFO] [2019-10-12 12:33:48] Assocs to occurrences...
[INFO] [2019-10-12 12:33:48] Assocs to nodes...
[INFO] [2019-10-12 12:33:48] Assoc to sex term...
[INFO] [2019-10-12 12:33:48] Assoc to lifestage term...
[STOP] [2019-10-12 12:33:48] resolve_keys
[START] [2019-10-12 12:33:48] hold_for_later_1
[STOP] [2019-10-12 12:33:48] hold_for_later_1
[START] [2019-10-12 12:33:48] hold_for_later_2
[STOP] [2019-10-12 12:33:48] hold_for_later_2
[START] [2019-10-12 12:33:48] resolve_missing_parents
[STOP] [2019-10-12 12:33:49] resolve_missing_parents
[START] [2019-10-12 12:33:49] rebuild_nodes
[START] [2019-10-12 12:33:49] Flattener#flatten
[START] [2019-10-12 12:33:49] Flattener#study_resource
[START] [2019-10-12 12:33:49] Flattener#build_ancestry
[STOP] [2019-10-12 12:33:49] Flattener#build_ancestry
[INFO] [2019-10-12 12:33:50] 1554 ancestry keys
[START] [2019-10-12 12:33:50] build_node_ancestors
[INFO] [2019-10-12 12:33:50] old ancestors deleted.
[STOP] [2019-10-12 12:33:50] build_node_ancestors
[START] [2019-10-12 12:33:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:33:50] Flattener#propagate_ancestor_ids
[STOP] [2019-10-12 12:33:50] Flattener#flatten
[STOP] [2019-10-12 12:33:50] rebuild_nodes
[START] [2019-10-12 12:33:50] resolve_missing_media_owners
[STOP] [2019-10-12 12:33:50] resolve_missing_media_owners
[START] [2019-10-12 12:33:50] sanitize_media_verbatims
[STOP] [2019-10-12 12:33:50] sanitize_media_verbatims
[START] [2019-10-12 12:33:50] queue_downloads
[STOP] [2019-10-12 12:33:50] queue_downloads
[START] [2019-10-12 12:33:50] parse_names
[WARN] [2019-10-12 12:33:50] I see 1554 names which still need to be parsed.
[STOP] [2019-10-12 12:33:52] parse_names
[START] [2019-10-12 12:33:52] denormalize_canonical_names_to_nodes
[STOP] [2019-10-12 12:33:52] denormalize_canonical_names_to_nodes
[START] [2019-10-12 12:33:52] match_nodes
[START] [2019-10-12 12:33:52] map_all_nodes_to_pages
[STOP] [2019-10-12 12:34:53] map_all_nodes_to_pages
[INFO] [2019-10-12 12:34:53] 28 Unmatched nodes (of 1554)! That's too many to output. First 10: Strumigenys emmae (#49379780); Ceriantharia (#49378846); Rhinesomus (#49379196); Siphonodictyon coralliphaga (#49380205); Scorpaeniformes (#49378978); Dendroica (#49379642); Dendroica petechia (#49379641); Mussidae (#49379736); Aratinga pertinax (#49379552); Neritopsina (#49379227)
[START] [2019-10-12 12:34:53] update_nodes
[STOP] [2019-10-12 12:34:54] update_nodes
[STOP] [2019-10-12 12:34:54] match_nodes
[START] [2019-10-12 12:34:54] reindex_search
[STOP] [2019-10-12 12:34:56] reindex_search
[START] [2019-10-12 12:34:56] normalize_units
[STOP] [2019-10-12 12:34:56] normalize_units
[START] [2019-10-12 12:34:56] calculate_statistics
[STOP] [2019-10-12 12:34:56] calculate_statistics
[START] [2019-10-12 12:34:56] complete_harvest_instance
[START] [2019-10-12 12:34:56] overall_tsv_creation
[INFO] [2019-10-12 12:34:56] Processing group of 1554 in 1 batches of 10000
[INFO] [2019-10-12 12:35:47] 482 Traits (unfiltered)...
[INFO] [2019-10-12 12:36:01] 482 Traits (filtered)...
[INFO] [2019-10-12 12:36:01] 0 Associations (filtered)...
[INFO] [2019-10-12 12:36:39] 2410 metadata added.
[INFO] [2019-10-12 12:36:39] 0 metadata added.
[INFO] [2019-10-12 12:36:39] Average Time: 81.1
[INFO] [2019-10-12 12:36:39] Total Time: 1m44s
[STOP] [2019-10-12 12:36:39] overall_tsv_creation
[INFO] [2019-10-12 12:36:39] Done. Check your files:
[INFO] [2019-10-12 12:36:39] (1554 lines) /app/public/data/curacao_sp_list/publish_nodes.tsv
[INFO] [2019-10-12 12:36:39] (2741 lines) /app/public/data/curacao_sp_list/publish_node_ancestors.tsv
[INFO] [2019-10-12 12:36:39] (1554 lines) /app/public/data/curacao_sp_list/publish_scientific_names.tsv
[INFO] [2019-10-12 12:36:39] (483 lines) /app/public/data/curacao_sp_list/publish_traits.tsv
[INFO] [2019-10-12 12:36:39] (2411 lines) /app/public/data/curacao_sp_list/publish_metadata.tsv
[STOP] [2019-10-12 12:36:39] complete_harvest_instance
[START] [2019-10-12 12:36:39] completed
[STOP] [2019-10-12 12:36:39] completed
[STOP] [2019-10-12 12:36:39] logged process, took 192.04
Latest Process

12 Oct 12:33 EXITED currently processing 0